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Modern Methods for Theoretical Physical
Chemistry of Biopolymers
by Evgeni Starikov (Editor), James P. Lewis (Editor),
Shigenori Tanaka (Editor)

• Pub. Date: August 2006

• ISBN: 0444522204
• Publisher: Elsevier Science & Technology Books
 List of Contributors

Shinji Amari
Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku,
Tokyo 153-8904, Japan

J. F. R. Archilla
Group of Nonlinear Physics, Departamento de Física Aplicada I, ETSI Informática,
University of Sevilla, Avda Reina Mercedes, s/n. 41012, Sevilla, Spain

David N. Beratan
Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708, U.S.A.

F. Matthias Bickelhaupt
Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit,
De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands

Johan Bredenberg
Karolinska Institutet, Department of Biosciences, Center for Structural Biochemistry,
Hälsovägen 7, SE-141 57 Huddinge, Sweden

Ralf Bulla
Theoretische Physik III, Universität Augsburg, D-86135, Augsburg, Germany

Arrigo Calzolari
National Centre on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR,
c/o Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A,
41100 Modena, Italy

Hiroshi Chuman
Institute of Health Biosciences, University of Tokushima, Tokushima, 770-8505, Japan

Peter Claiden
Department of Materials Science and Metallurgy, University of Cambridge, Pembroke
Street, Cambridge CB2 3QZ, UK

Daniel L. Cox
Department of Physics, University of California, Davis, CA 95616, U.S.A.
v
vi List of Contributors

Tobias Cramer
Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104
Freiburg im Breisgau, Germany

Jane Crawshaw
Department of Materials Science and Metallurgy, University of Cambridge, Pembroke
Street, Cambridge CB2 3QZ, UK

Gianaurelio Cuniberti
Institut für Theoretische Physik Korrelationen und Magnetismus, Universität
Regensburg, D-93040, Regensburg, Germany

Martin Dahlberg
Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91,
Stockholm, Sweden

Owen R. Davies
School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3YB, UK

James Elliott
Department of Materials Science and Metallurgy, University of Cambridge, Pembroke
Street, Cambridge CB2 3QZ, UK

Robert G. Endres
Department of Molecular Biology, Princeton University, Princeton, NJ 08544-1014, U.S.A;
and NEC Laboratories America, Inc., Princeton, NJ 08540 U.S.A.

Dmitri G. Fedorov
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono,
Tsukuba, 305-8568 Ibaraki, Japan

Rosa Di Felice
National Centre on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR,
c/o Dipartimento di Fisica, Università di Modena e Reggio Emilia, Via Campi 213/A,
41100 Modena, Italy

B. Fischer
Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, Postfach 3640,
D-76021 Karlsruhe, Germany

Kaori Fukuzawa
Division of Science and Technology, Mizuho Information & Research Institute, Inc., 2-3
Kanda Nishiki-cho, Chiyoda-ku, Tokyo 101-8443, Japan; and CREST, Japan Science and
Technology Agency (JST), Japan
List of Contributors vii

Yi Qin Gao
Department of Chemistry, Texas A&M University, College Station, TX 77845, U.S.A

Heather L. Gordon
Department of Chemistry and Centre for Biotechnology, Brock University, St. Catharines,
Ontario, L2S 3A1, Canada

Hitoshi Goto
Department of Knowledge-based Information Engineering, Toyohashi University of
Technology, Toyohashi, 441-8580, Japan

Célia Fonseca Guerra

Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit,
De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands

Rafael Gutierrez
Institut für Theoretische Physik Korrelationen und Magnetismus, Universität Regensburg,
D-93040, Regensburg, Germany

Michiaki Hamada
Mizuho Information and Research Institute, Inc., Tokyo, 101-8443, Japan

D. Hennig
Freie Universität Berlin, Fachbereich Physik, Institut für Theoretische Physik, Arnimallee
14, 14195 Berlin, Germany

Arnd Hübsch
Department of Physics, University of California, Davis, CA 95616, U.S.A.

Yuichi Inadomi
Grid Technology Research Center, National Institute of Advanced Industrial Science and
Technology, Tsukuba, 305-8568, Japan

Yuichiro Inagaki
Mizuho Information and Research Institute, Inc., Tokyo, 101-8443, Japan

John E. Inglesfield
School of Physics and Astronomy, Cardiff University, Cardiff, CF24 3YB, UK

Masakatsu Ito
Grid Technology Research Center, National Institute of Advanced Industrial Science and
Technology, Tsukuba, 305-8568, Japan
viii List of Contributors

Toshiyuki Kamakura
Department of Knowledge-based Information Engineering, Toyohashi University of
Technology, Toyohashi, 441-8580, Japan

Martin Karplus
Deparment of Chemistry and Chemical Biology, Harvard University, MA 02138, U.S.A;
and Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 67000
Strasbourg, France

Kazuo Kitaura
National Institute of Advanced Industrial Science and Technology, 1-1-1 Umezono,
Tsukuba, 305-8568 Ibaraki, Japan

Thorsten Koslowski
Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104
Freiburg im Breisgau, Germany

Petras J. Kundrotas
Department of Biosciences at Novum Research Park, Karolinska Institutet, SE-141 57
Huddinge, Sweden

Noriyuki Kurita
Department of Knowledge-Based Information Engineering, Toyohashi University of
Technology, Toyohashi, Aichi 441-8580, Japan

Aatto Laaksonen
Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S 106 91,
Stockholm, Sweden

Victor D. Lakhno
Institute of Mathematical Problems of Biology, Russian Academy of Sciences,
Pushchino, Moscow Region, 142290, Russian Federation

K. H. Lee
Korean Institute for Science and Technology, Supercomputing Materials Laboratory,
P.O. Box 131, Cheongryang, Seoul 130-650, Korea

J. P. Lewis
Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602-
4658, U.S.A.

Jianping Lin
Departments of Chemistry and Biochemistry, Duke University, Durham, NC 27708,
U.S.A.
List of Contributors ix

Raimo A. Lohikoski
University of Jyväskylä, Department of Physics, FIN - 40014 University of Jyväskylä,
Finland

Pekka Mark
Karolinska Institutet, Department of Biosciences, Center for Structural Biochemistry,
Hälsovägen 7, SE-141 57 Huddinge, Sweden

R. Marsh
Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602-
4658, U.S.A.

H. Merlitz
Forschungszentrum Karlsruhe GmbH, Institut für Nanotechnologie, Postfach 3640,
D-76021 Karlsruhe, Germany

Yuji Mochizuki
Advancesoft and Institute of Industrial Science, Center for Collaborative Research, The
University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan; Institute of
Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904,
Japan; and CREST, Japan Science and Technology Agency (JST), Japan; Department of
Chemistry, Faculty of Science, Rikkyo University, 3-34-1 Nishi-ikebukuro, Toshima-ku,
Tokyo 171-8501, Japan

Umpei Nagashima
Grid Technology Research Center, National Institute of Advanced Industrial Science and
Technology, Tsukuba, 305-8568, Japan

Yoshihiro Nakajima
Center for Computational Sciences, University of Tsukuba, Tsukuba, 305-8577, Japan

Tatsuya Nakano
Division of Safety Information on Drug, Food and Chemicals, National Institute of
Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan; Institute of
Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-
8904, Japan; and CREST, Japan Science and Technology Agency (JST), Japan

Naofumi Nakayama
Department of Knowledge-based Information Engineering, Toyohashi University of
Technology, Toyohashi, 441-8580, Japan

Takayuki Natsume
Department of Knowledge-Based Information Engineering, Toyohashi University of
Technology, Toyohashi, Aichi 441-8580, Japan
x List of Contributors

Lennart Nilsson
Department of Biosciences at NOVUM, Center for Structural Biochemistry, Karolinska
Institutet, S-141 57 Huddinge, Sweden; Karolinska Institutet, Department of Biosciences,
Center for Structural Biochemistry, Hälsovägen 7, SE-141 57 Huddinge, Sweden

Takeshi Nishikawa
Grid Technology Research Center, National Institute of Advanced Industrial Science and
Technology, Tsukuba, 305-8561, Japan

Sigeaki Obata
Department of Knowledge-based Information Engineering, Toyohashi University of
Technology, Toyohashi, 441-8580, Japan

Miroslav Pinak
Japan Atomic Energy Agency, Shirakata, Shirane 2-4, 319-1195 Tokai, Japan

Dragan M. Popovic
Department of Chemistry, University of California, One Shields Avenue, Davis, CA
95616, U.S.A.

Jason Quenneville
Department of Chemistry, University of California, One Shields Avenue, Davis, CA
95616, U.S.A.

Aina Quintilla
Research Center Karlsruhe, Institute for Nanotechnology, D-76021 Karlsruhe,
Germany

R. A. Römer
Department of Physics and Centre for Scientific Computing, University of Warwick,
Coventry CV4 7AL, U.K.

Stuart M. Rothstein
Departments of Chemistry and Physics, Brock University, St. Catharines, Ontario, L2S
3A1, Canada

Mitsuhisa Sato
Center for Computational Sciences, University of Tsukuba, Tsukuba, 305-8577,
Japan

Matthias Schmitz
Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians
Universität München, Oettingenstraße 67, 80538 München, Germany
List of Contributors xi

A. Schug
Forschungszentrum Karlsruhe, Institute for Nanotechnology, P.O. Box 3640, D-76021
Karlsruhe, Germany

Yasuo Sengoku
Department of Knowledge-Based Information Engineering, Toyohashi University of
Technology, Toyohashi, Aichi 441-8580, Japan

Rajiv R. P. Singh
Department of Physics, University of California, Davis, CA 95616, U.S.A.

Spiros S. Skourtis
Department of Physics, University of Cyprus, Nicosia 1678, Cyprus

Evgeni B. Starikov
Department of Chemistry, Freie Universität Berlin, Germany; Department of Structural
Biology at NOVUM, Karolinkska Institute, Huddinge, Sweden; and Research Center
Karlsruhe, Institute for Nanotechnology, D-76021 Karlsruhe, Germany

Alexei A. Stuchebrukhov
Department of Chemistry, University of California, One Shields Avenue, Davis, CA
95616, U.S.A.

Shigenori Tanaka
Graduate School of Science and Technology, Kobe University, 1-1, Rokkodai, Nada-ku,
Kobe 657-8501, Japan; and CREST, Japan Science and Technology Agency (JST),
Japan

Paul Tavan
Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians
Universität München, Oettingenstraße 67, 80538 München, Germany

Nadine Utz
Institut für Physikalische Chemie, Universität Freiburg, Albertstrasse 23a, D-79104
Freiburg im Breisgau, Germany

A. Verma
Forschungszentrum Karlsruhe, Institute for Scientific Computing, P.O. Box 3640,
D-76021 Karlsruhe, Germany

Alexander A. Voityuk
Institució Catalana de Recerca i Estudis Avançats, Institute of Computational Chemistry,
Universitat de Girona, 17071 Girona, Spain
xii List of Contributors

H. Wang
Department of Physics and Astronomy, Brigham Young University, Provo, UT 84602-
4658, U.S.A.

Toshio Watanabe
Grid Technology Research Center, National Institute of Advanced Industrial Science and
Technology, Tsukuba, 305-8568, Japan

Wolfgang Wenzel
Research Center Karlsruhe, Institute for Nanotechnology, D-76021 Karlsruhe, Germany;
Forschungszentrum Karlsruhe, Institute for Nanotechnology, P.O. Box 3640, D-76021
Karlsruhe, Germany

Alan Windle
Department of Materials Science and Metallurgy, University of Cambridge, Pembroke
Street, Cambridge CB2 3QZ, UK

Wei Yang
Deparment of Chemistry and Chemical Biology, Harvard University, MA 02138, U.S.A
 Foreword
Biopolymers, such as nucleic acids, proteins and polysaccharides, are the functional
basis of all forms of life on Earth. Their three-dimensional structures provide the ro-
bustness needed to form templates for parts that constitute biochemical function. At the
same time, the dynamics of biopolymers are also crucial, first for folding them into their
active conformations and, second, dynamics itself may often play an active role in func-
tion. While the connection between structure and function is widely recognized among
biochemists, as indicated by the frequently used ‘key-in-lock’ metaphor, the dynamics
counterpart is less well explored and understood – much due to the lack of sufficiently
selective and accurate experimental methods and results. Here computational chemistry
has for some time played a major role in testing and visualizing models of conforma-
tional molecular dynamics and also processes involving proton or electron transfer re-
actions, and has become an invaluable complement to experimental structural tools,
such as NMR or X-ray crystallography, for assessing equilibrium structures in solution
and solid state, respectively.
In addition to the traditional scientific areas connected with the study of biological
macromolecules, there are a number of young, yet actively expanding fields, involving
biopolymers: nanoscience, biotechnology and molecular medicine. In nanoscience and
molecular biotechnology, biopolymers and related compounds may be used as templates
or scaffolds for various miniaturized technologies – a field which requires detailed
knowledge about the structure, dynamics and interactions of the molecules. For instance,
hybridization schemes of nucleic acids may be used for designing addressable molecular
node assemblies on soft-matter surfaces, which in turn may have applications for making
molecular electronics, microscopic molecular machines, diagnostic devices and so on. In
the area denoted molecular medicine, specific proteins, whose conformational variabil-
ity may be related to serious health disorders like Alzheimer’s, Parkinson’s, Huntington’s
and Creutzfeld–Jacobs diseases, are dealt with. Also here knowledge about structure, dy-
namics and interactions of these molecules is needed for understanding the mechanistic
background of these deficiencies.
What is clear throughout, and widely accepted, is that biopolymers are extremely com-
plicated physical objects. In order to meet the needs of the above-mentioned scientific
branches, broad approaches including several parallel experimental and theoretical tech-
niques are generally necessary. Very frequently, however, the existing experimental meth-
ods, even at their modern, tremendously high level of sophistication, are not sufficiently
selective to embrace all the interesting aspects of the biopolymer-related phenomena under
study. Indeed, this is usually the case when it comes to studies on ultra-fast kinetics of en-
zymatic reactions, of charge transport through biopolymers, etc. Instead, one is referred to
computational approaches for getting a more complete description and understanding of
such complex systems. Also, the biopolymers are themselves very complicated dynamical
systems, with lots of degrees-of-freedom at a variety of time scales, from femto-seconds
up to seconds range. To untangle all these dynamics, for example, to be able to character-
ize just one dynamic variable at a time, within the frame of some particular experimental
study on biopolymers or their complexes, is in most cases even in principle impossible.
xxvii
xxviii Foreword

Bearing all this in mind, the importance of theoretical studies on biopolymers, their
components and related compounds for fully fledged scientific research on them may
hardly be exaggerated. Nowadays, theoretical and computational methods in this field are
quite well developed, being vigorously stimulated by the dramatic improvements and in-
crease in modern computing power.
This multi-author book, edited by Starikov, Tanaka and Lewis, provides an interesting
selection of contributions from a wide international team of high-class researchers rep-
resenting the main theoretical areas useful for tackling the complicated scientific prob-
lems connected with biopolymers’ physics and chemistry. It exemplifies the applications
of both the classical molecular-mechanical and molecular-dynamical methods, as well as
the quantum chemical methods needed for bridging the gap to structural and dynamical
properties dependent on electron dynamics. It also provides nice illuminations on how to
deal with complex problems when all three approaches need to be considered at the same
time. The book gives a rich spectrum of applications: from theoretical considerations of
how ATP is produced and used as ‘energy currency’ in the living cell, to the effects of
subtle solvent influence on the properties of biopolymers, and how structural changes in
DNA during single-molecule manipulation may be interpreted. As an experimental phys-
ical chemist active in the biopolymers field I do appreciate this effort to give an interest-
ing introduction to the currently available theoretical methods.

Bengt Nordén
President of the Fourth Class (Chemistry) of the Royal Swedish Academy of Sciences
and former Chairman of its Nobel Committee for Chemistry
 Preface
While working out the general concept for the present publication, we never thought of
it as an exhaustive handbook, nor did we plan to write a detailed course book. Instead, its
main purpose is to show the modern successes and trends in theoretical physical chem-
istry/chemical physics of biopolymers. Hence, in our minds, the main readership should
consist of senior pre-graduates, doctoral students, and younger postdocs in the latter
fields, although it would definitely be an utmost honor to us, if those experienced, pro-
fessional theorists–who are involved in biophysical, structural biological, bionanotech-
nological, or other related studies–could still find several interesting and novel aspects
here. With this in mind, we have encountered a formidable task of carefully selecting the
most important contributions to the field, so that the result is inevitably more or less a
product of our subjective choice. Nevertheless, we hope that colleagues, whose important
and interesting work on biopolymers has not found its proper reflection here, will not get
angry with us, the Editors.
For the sake of convenience, we have divided the book into several logical parts, each
of which includes a number of chapters written by renowned specialists in their corre-
sponding fields. The succession of these parts represents the actual guideline showing the
recommended direction for reading the book, although those colleagues who may be in-
terested in only one aspect or several particular aspects might easily skip all unnecessary
material without hindering their proper understanding of that particular area.
The first and foremost part of the book deals with quantum chemical studies on
biopolymers and their models, since the most general theory describing properties of any
molecule is quantum mechanics. Quantum chemistry is a well-known and well-tried way
of approximating a quantum mechanical description of molecular electronic structures.
However, when it comes to studying very long oligo (or poly)mers, the conventional
quantum chemical ‘machinery’ often fails, owing to complex computational tasks not
quite amenable even to the newest computers. This poses a problem of attracting further
likely approximations, which could make the quantum chemical studies of large biomol-
ecules more feasible.
One of the ways to solve the latter problem is discussed in detail in Chapter 1, de-
scribing the mathematical and computational foundations of the so-called FMO (frag-
ment molecular orbital) method. Interestingly, the latter has already been proven to pro-
vide a reliable tool for investigating the electronic structure, intermolecular interactions,
and even electron absorption spectra of large biomolecules. Interested readers can find
a more detailed description of this in Chapter 2.
While the FMO method pretends to preserve the fully fledged quantum chemical level
of molecular description, a more popular approach tends to select a relatively restricted
and small region within a biomacromolecule, which can be treated in a rigorous quantum
chemical way, whereas the vast majority of the biopolymer in question, together with its
solvent surrounding, is considered a classical molecular–mechanical/dynamical system
and/or a source of electrostatic field acting on the quantum chemical subsystem. Such
‘hybrid’ approaches, usually dubbed QM/MM (quantum mechanical/molecular me-
chanical), are proven to be extremely useful. For example, this is useful when studying
xxix
xxx Preface

chemical processes in reactive pockets of enzymatic proteins, and also in one of the ex-
amples given in Chapter 3.
Along with this, it must be stressed that the usefulness of the conventional quantum
chemical approaches for solving modern biomolecular problems should in no way be un-
derestimated, as clearly demonstrated in Chapter 4 (which discusses the details of the
physical–chemical nature of Watson–Crick hydrogen bonds in nucleic acids) and Chapter
5 (which discusses the quantum chemical evaluation of charge transfer parameters in nu-
cleic acids).
Still, a great number of biologically relevant problems involving biopolymers can be
solved by assuming solely classical mechanical (purely MM) pictures and avoiding any
thorough quantum chemical description, with conformational preferences/dynamics, rhe-
ology and folding of, docking small molecules to, structural defects in biomacromole-
cules, biomolecular motors, etc. among them. In our opinion, good examples of such
studies are presented in Chapters 6–13. On the one hand, the solution of large-scale prob-
lems, like drug discovery, requires involvement of the modern computational technolo-
gies (for grid technologies, see Chapter 12). The models of the latter sort must in many
cases be used in clever combinations with the molecular mechanical and/or molecular
dynamical approaches in the all-atom representation (like in investigations of molecular
motors, where molecular dynamics are combined with kinetic equations, see Chapter 14).
Of course, the intricate complexity of biopolymers also allows us to sometimes di-
rectly treat them as statistical/stochastic systems and/or to use statistical methods in de-
scription or elucidation of their properties. One of the areas of effective and successful
applications of statistical methods, like Monte Carlo (Chapter 14), principal component
(factor) analysis (Chapter 15), as well as stochastic optimization techniques (Chapter 16),
is connected with elucidating the detailed mechanisms of protein folding.
Aside from all the above-mentioned methods and concepts of biophysical chemistry,
there is one unique theme which belongs to the field of biochemical physics, namely,
charge transfer/transport in and electrical properties of biomacromolecules, with special
reference to DNA. The latter phenomenon is still fiercely debated, and thus stimulates in-
tensive and numerous physical–chemical theoretical studies.
The general physical basis of such studies is the so-called ‘tight-binding’ approxima-
tion, where large biomolecular fragments like, for example, Watson–Crick base pairs in
DNA, are declared to be just abstract ‘sites’ carrying only one orbital which describes
electron motions within each ‘site’. Chemically, these orbitals correspond to either
HOMO (the highest occupied molecular orbital) or LUMO (the lowest unoccupied mo-
lecular orbital). The sites involved are then characterized by their ‘site energy,’ which is
either ionization potential (the energy required to withdraw one electron from the site if
the site orbital is HOMO) or electron affinity (the energy required to add one electron to
the site if the orbital is LUMO).
In real biopolymers, these sites are coupled to each other, and it is this electronic cou-
pling that promotes the motion of the added electron, or a positively charged ‘hole’ pro-
duced by withdrawing one electron. Since there is always a discrete set of such sites, the
motion of the charged particle is just hopping from one site to another. This is why the
strength of electronic coupling (the term preferred by chemists) between the neighboring
sites is frequently called ‘hopping parameter’ or ‘hopping integral’ (the term preferred by
Preface xxxi

physicists), and in most cases it is silently or explicitly assumed that the hopping can only
occur between the nearest-neighboring sites. To establish a connection between the above
oversimplified model and the actual bipolymer systems, one needs to have likely estimates
of the site energies and hopping integrals (alias electron couplings). In solving this prob-
lem, quantum chemistry is very effective (as we have already seen in Chapter 5, but see
also in Chapters 18–24). Model Hamiltonians are very important not only in describing
electronic structure of biopolymers, but also their classical mechanical and dynamical
properties. This is clearly demonstrated in the Chapter 17, where phenomenological, ana-
lytically solvable models (mechanical soliton models) are described.
Meanwhile, to provide one with a completely valid description of the biomacromolecu-
lar charge transfer/transport, the rigid in vacuo set of the above-mentioned ‘sites’ is by far
not enough. Indeed, the conformational degrees-of-freedom, as well as the water–counter-
ion environment, of biopolymers must also be taken into account by any correct physical
theory (see an excellent review of this theme in Chapter 18). There are basically two ways
to achieve this, namely, either to assume some functional dependence of the site energies
and hopping parameters on the intra-biopolymer degrees-of-freedom and dynamical modes
of the surrounding, or to treat the the dynamics of the biopolymer together with its envi-
ronment explicitly, by using classical molecular dynamics in the all-atom representation.
The first approach enables one to formulate so-called polaron theories of the charge
transport, if site energies and hoppings can be considered linear functions of the confor-
mational degrees-of-freedom, so that the charge motion can be viewed as a propagation
of a charged particle, which permanently ‘drags’ the biopolymer ‘lattice’ deformation
with itself (the picture most popular among physicists). The parameters of coupling be-
tween the charged particle motion and the biopolymer ‘lattice’ deformation can also be
estimated using a clever combination of quantum chemistry and classical molecular dy-
namics in the all-atom representation (see also Chapter 5, as well as Chapters 19–24).
The second approach makes it possible to direct simulation of the charge
transfer/transport process, which helps us to visualize it (the picture most popular among
chemists, see Chapters 20–22 and 24).
More exciting details on how all of the above approaches and ideas work in real phys-
ical studies can be found in Chapters 18–24.
The last, but not least, area of modern biopolymers theory is concerned with their
electrical properties, which are of primary importance for modern bionanoscience. This
theme is related to model Hamiltonians from the previous book section, but there are still
some very important differences. Namely, the tight-binding Hamiltonians are very good
at describing the propagation of a single charge particle through biopolymers, which is
completely relevant to experiments carried out by physical chemists. However, if we wish
to consider the full physical–technical representation of electrical properties of bio-
macromolecules, we must also consider charge flows in them, created by attaching them
to electrodes and applying voltage. The latter situation requires a different electric trans-
port theory, compared with the former case. Chapter 25 shows in detail, how density-
functional theory (DFT) can be used in trying to solve the latter problem. Chapters 26
and 27 present detailed accounts of such theories and algorithms in the all-atom repre-
sentation. The difference between the two approaches–outlined in the last two chap-
ters–consists of the accuracy and efficiency of biomolecular description.
 Another Random Document on
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walls of which shine with gold,
and the pavement with
precious marble. In the midst
of it is an inclosure of four
chains, which proceed from the
aforesaid four churches, and in
it said to be the centre of the
world.”

88. Williams’ ‘Holy City,’ ii., 264.

With a very few trifling exceptions, which may be found

enumerated in the ‘Bible Atlas,’ p. 73, the whole voice of writers
since the tenth century is clearly and unmistakably in favour of the
present site.
We must not omit to notice the opinion of Mr. Lewin, that the
Dome of the Rock was originally the Temple of Jupiter, which Dion
Cassius tells us was built on the site of Herod’s Temple. But he goes
on to suppose that Hadrian was deceived as to the real situation of
the Temple, a thing which seems to us impossible. The foundations
which the Mohammedans found when they began to build, may very
well have been those of the Temple of Jupiter, and many of the old
pillars may have been used for the new Dome. The destruction of
the Temple was probably due to Chosroes, who clearly left nothing
standing at all. It may, however, have been destroyed by the pious
zeal of the Christians.
So far therefore, as the historical evidence goes, it appears to us
that the following facts come out with great clearness.
(1.) Josephus, and therefore the Jews generally, believed that
Solomon’s temple was built on the highest part of the hill, the
ground being afterwards raised artificially.
(2.) Herod’s temple was built, with greater magnificence, in the
same spot.
(3.) Hadrian built a temple to Jupiter on the Temple Hill.
(4.) Julian attempted to rebuild the temple itself from its old
foundations. Did he, to effect this object, first destroy the Temple of
Jupiter? If not, who did?
(5.) For four centuries after this the place remained a receptacle
for filth of all kinds, but not forgotten.
(6.) Omar erected a small mosque in front of it (p. 76).
(7.) ‘Abd el Melik and his successors repaired the whole Masjid
(the Haram Area), built the Mosque el Aksa, and the Dome of the
Rock (p. 79).
(8.) The Crusaders called the Dome of the Rock, Templum Domini,
the Temple of the Lord, to distinguish it from the Mosque el Aksa,
which they called Templum Solomonis, the Palace of Solomon.
With regard to the Church of the Holy Sepulchre, we have the
following data furnished us.
(1.) Constantine decorated the cave, and erected a magnificent
Basilica over the site of the Crucifixion.
(2.) All Constantine’s buildings were destroyed by Chosroes; and
rebuilt, after a fashion, by Modestus, with the assistance of John
Eleemon, Patriarch of Alexandria.
(3.) The Mohammedans at the taking of the city spared the
Church of the Holy Sepulchre.
(4.) Hakem ordered the destruction of the church. This was done,
and collections were made in every part of the Christian world to
rebuild it.
(5.) This church was burned down in 1808.
With regard to the discrepancies in the accounts given by pilgrims,
and the impossibility of completely harmonizing their descriptions
with any theory of sites, this may be remarked: Too much stress
must not be laid upon the accuracy or inaccuracies of stories told by
early travellers. Why should we look for accuracy in the narrative of
a pilgrimage spent in a state of mental exaltation, of which we cold-
blooded Christians can have no possible idea? When the pilgrim,
arrived at the goal of his journey, was crawling on his knees from
site to site, praying and praising, abandoning himself to all the
emotions which the memories of the places evoked, was it a time to
pull out the measuring tape and to count the paces?
To sum up, next, the historical evidence as regards the Dome of
the Rock.
 (1.) When Mohammedan writers speak of the Masjid el Aksa, they
mean, not the Mosque el Aksa, but the whole Haram Area, including
all the oratories, mosques, minarets, &c.
(2.) All these were built, as has been related, chap. IV., by ‘Abd el
Melik.
(3.) The Dome of the Rock is only a supplementary building (see
p. 83).
(4.) When the pulpit, the ‘kiblah,’ &c., of the Masjid el Aksa is
spoken of, we must refer it to the Jami‘ el Aksa.
The Haram Area, when Omar visited it first, presented an aspect
somewhat similar to what it has at present, so far as its outward
walls, dimensions, and general level are concerned. In the centre
was the rock, where, as everybody knew, had been the Temple. This
was covered with rubbish and filth. And round the rock, and about it,
were certain old foundations, most likely those of Hadrian’s Temple
to Jupiter, possibly those of the Temple of Herod. Along the south
wall were extensive ruins. At the south-east angle lay arches and
substructures overthrown; and further west the ruins of a Christian
church, most probably that of Justinian’s church, now the Jami‘ el
Aksa. All these substructures were repaired by the Mohammedans,
the position of the walls being, naturally, retained. Then, being
desirous of building a dome over the Sacred Rock, ‘Abd el Melik
issued letters and collected money. He first designed and built a
small dome, the same which is now called the Cubbet es Silsilah, for
a treasury. He was so pleased with the work that he ordered his
great dome to be built on the same model. The Dome of the Rock
must not be compared with other mosques, because it is not one,
and was never meant for one, but it may advantageously be
compared with other welis, or Mohammedan oratories. Therefore no
argument can be drawn from what would be an exceptional shape
for a mosque.
It must be distinctly understood that Arabic historians are as clear
and explicit as to the building of this splendid dome as we should be
over the building of St. Paul’s by Christopher Wren; and that in the
account given by us (p. 79 et seq.) no single sentence is inserted for
which there is not full authority in the Arabic historians.
 The third and last method of argument is from architecture.
History may be misinterpreted. It may even purposely deceive.
But architecture cannot lie. Within limits, superior and inferior,
the date of a building can be assigned to it. These limits
approach each other more nearly as we come to modern times.
Architects find no difficulty, for instance, in distinguishing
buildings of the fifteenth from those of the sixteenth century. But
the limits recede from each other as we go back. Therefore it is
that this is an argument, as concerns the Holy Sepulchre, which
can only be used by hands of the greatest experience. Nor ought
any conclusion to be generally accepted by the world until it has
been acceded to by a majority of that small number of architects
competent to judge. Mr. Fergusson has written on the
architecture of the Dome of the Rock; his conclusions however
have not met with the approval of authorities, such as Professor
Willis, or the Count de Vogüé, of equal rank with himself. Until
architects agree, then, surely we have nothing to rest on but the
historical evidence.
 INDEX.

Abu Bekr, 66
Abu ’l Casím, 431
Abu ’l Faraj, 430
Abu ’l Fath Nasr, 431
Abu Ishak, 428
Abu Obeidah, 70, 423
Abu Saíd Barkúk, 435
Abu Táher, 95
Abúdat ibn es Sámit, 424
Abyssinians, 475
Acre, 367, 391, 406, 464
Adana, 166
Adhémar, 144, 145, 171, 173, 175
Ælia Capitolina, 54
Afdhal, 196, 330
Agrippa, chap. i.
Akiba (Rabbi), 51
Albinus, 8
Alexandria surrenders to Shirkoh, 307;
taken by Amaury, 308
Alexis Comnenus, chap. vi.
Alice of Antioch, 253, 261
Alimi, El, 438
Al Imám es Shafi, 429
Amaury, King, chap. xiv.
Amaury de Lusignan, 444
Andrew’s Crusade, 451
Anselm, vision of, 178
Antioch, siege of, 170
Antoninus, 118
Arabs, their character and arts, 91
Armenians, 475
Arm of Ambrose, loss of, 207
Arnold, 176, 185, 216
Arnulphus, 118
Ascalon, 107, 287, 408
Ashraf Barsebai, Sultan, 435
—— Catibai, Sultan El, 439
—— Einál, Sultan El, 438
—— Shaban, Es Sultan, 434
Assassins, murder of messenger, 319;
sect of, 322
Assises de Jerusalem, 202

Babain, battle of, 307

Baghi Seyan, 170
Baldwin I., chap. viii., 166, 201
—— II., chap. ix.
—— III., chap. xi., 269
—— IV., chap. xiii.
—— V., 343
Baldwin du Bourg, 225, 231, and chap. ix.
Balian of Ibelin, 352
Barcochebas, 52
Battle of Lake Huleh, 292
Bedawín in Jerusalem, 441
Beirût, attempt on, 413
Bellál ibn Rubáh, 424
Benjamin of Tudela, 328
Berenice, 14
Bernard, 277
Bertram of Tripoli, 227
Bertrand de Blanqueford, 310
Bether, 53
——, identification of, 54
Beyrout, 10
——, taking of, 228
Bir el Warakah (Well of the Leaf), 421
Bishop’s Pilgrimage, 136
Blanchegarde, 267
Bohemond, 156, 224
Bordeaux Pilgrim, 116
Burham-ed-dín, Sheik, 437
Burzíyeh, castle of, 395

Cadam es Sheríf, 419

Cadhi of Jerusalem, 437
Cæsarea, 7, 16, 179, 219
Calaun, Es Sultan, 434
Caliph of Cairo, 305
Carmathians, the, 95
Carrier pigeons, 401
Cestius Gallus, 10;
defeat of, 17
Chain, ordeal of the, 420
Charlemagne, 123
Chiefs of First Crusade, 135
Children’s Crusade, 448
Chosroes takes Jerusalem and destroys Church of Holy
Sepulchre, 63
Christians of city imprisoned, 441
Claudius Felix, 6
Clermont, Council of, 144
Cœnaculum, 436
Coloman, King, chap. vi.
Completion of Temple, 9
Conrad of Tyre, 367
Constance of Antioch, 288
Constantine builds Basilica, 59;
decrees against Jews, 60
Copts, 475
Cruelty of Christians, 404, 406
Crusades, time ripe for, 169
Crusaders, return of, 199
Cubbet el Míráj, 420
Cuspius Fadus, 3

Dagobert, 201, 214, 216, 217, 222

Damascus, siege of, 283
Damietta, 452
——, Greek fleet at, 315
Darúm, capture of, 411
Dhaher Chakmak, El Melik, 435
——, El Melik el, 433
Dhia-ed-Dín, 432
Dome of the Rock, erection of, 79;
repair of, 83, 93;
inscription in, 86;
not a mosque, 85
Druzes, their teaching, 106

Earthquake in Palestine, 316

Eastern Cloisters, 9
Edessa, fall of, 272
Edgar Atheling, 155
Edrei, 273
Effects of Christian occupation, 245
El Adhed, 332
El Arish, 233
El Emád, 387
El Ghazálí, 432
Eleanor, Queen, 281
Emico, 151
End of the world expected, 133
Es Sirát, Bridge of, 422
Eusebius, 57, et seq.
Eustace de Bouillon, 237
—— Garnier, 239
Ezz-ed-dín, 438

Fair of September, 127

Fakhr-ed-dín, 456
Fálek-ed-dín, 411
Famine in Egypt, 445
—— in city, 439
Fatemite Caliphs, 300
Festus, 8
Florus, Gessius, 10, 11, 12, 13
Foulcher de Chartres, 213
Fragrant herb, consecration of the, 427
Francis of Assisi, 458
Frederic D. of Swabia, 367
Frederick II., 453
—— Redbeard, 365
Freisingen, Bishop of, 280
Frotmond, story of, 124
Fulke, chap. x., 254
—— the Black, 133
—— de Neuilly, 445

Garnier de Grey, 211

Georgians, 476
Gessius Florus, 10
Ghars-ed-dín, 439
Godfrey, chap. vii., 154, 181
Gorgona, disaster in Valley of, 164
Gotschalk, 151
Gregory IX., 454
Guy de Lusignan, chap. xiv., 339
Guymer, 167

Hadrian, 51;
builds Temple of Jupiter on site of Temple, 54
Hajj, the, 417
Hakem, el, 99, 129
Haram repaired, 442
Harûn Er Raschíd, 123
Helena, Life of, 55;
Invention of the Cross, 56
Henry of Champagne, 367, 369, 443
Heraclius, 64, 67, 68
—— the Patriarch, 341
Hisam-ed-dín, 438
Holy Fire, miracle of, 216
Holy Grail, the, 219
Holy Lance, vision of the, 173;
discovery of, 174
Holy Sepulchre, discovery of, 57;
adornment of, 58
Hugh of Cæsarea, 304
—— of Jaffa, 263
—— Vermandois, 157, 205, 209
Humphrey de Toron, 346, 394

Ida of Austria, 209

Ilgazi, 238
Imposture of Easter fire, 474
Innocent III., 445
Interdicts in Palestine, 290

Jamí-en-Nisá, 421
Jerome, 114
Jerusalem, Repair of the walls, 410
—— Siege of, by Titus, chap. ii.
—— Siege and fall of, 354
—— Taking of, by Saladin, 385
Jesus, son of Ananus, 25
Jews, heroism of, 44
Jocelyn, 239, 241, 260
—— II., 271
John de Brienne, 446, 452
—— Comnenus, 265
—— of Gischala, chap. ii.
Josephus, chap. ii
Judas the Galilæan, 3
Julian, attempts to rebuild the Temple, 61

Ka‘abeh, the, desertion of, 96

Khalit ibn el Walíd, 424
Kharezmians, 459
Khotbah of Muhiy-ed-dín, 388
King, choice of, 191
Knights Hospitallers, foundation of, 247
—— Templars, foundation of, 249
Kokeb, capture of, 397

Lietbert, 135
Longsword, William, 337
Louis VII., chap. x.
—— IX., 461

Macám en nebé, 421

Macarias, 135
Maghárah, the, 419
Manahem, 15
Manners of the Syrian Christians, 295
Maria of Constantinople, 309
Masjid el Aksa, 75, 381
Mejír-ed-dín, 439
Milan, Bishop of, 206;
his army entirely destroyed, 207
Milicent, 263, 270, 293
Milo de Plancy, 336
Moazzem, El Melik el, 433
Modern city, chap. xix.
—— native Christians, 473
—— Jews of Jerusalem, 476
Mohammedan beliefs, 422
—— pilgrims, chap. xvii.
Mohammed ibn Karrám, 430
——, Sultan, 434
Montferrat, assassination of Marquis of, 369, 410
Montreal, capture of, 302
Mount Tarsus, passes of, 169

Nahr el Casb, battle of, 407

Nasir-ed-dín, 438
Nasír Farj, Sultan, 435
Naval defeat of Mohammedans, 392
Nero, 8
Nevers, Duke of, 208;
defeat of, 209
—— Count of, 309
Nicæa, battle of, 153;
siege of, 162
Nicephorus Phocas, 97, 128
Nicolas, preacher, 447
Nûr-ed-dín, 284, 292, 294, 301, 303, 309, 319, 327
Nuseiríyeh, doctrines of the, 425

Odolric, 132
Omar, Caliph, 68, et seq.
Ordeal by fire, 177
Order of St. Lazarus, 247

Pancrates, 168
Paula and Eudoxia, 114
Penances, 446
Peregrinationes, majores et minores, 121
Peter the Hermit, 141, and throughout chap. vi.
Philip Augustus, 365
—— of Flanders, 337
Pilgrim’s Progress, The, 118
—— service, the, 120
Pilgrimage, passion for, 113
Plague in Jerusalem, 441
Pons of Tripoli, 265
Population of Jerusalem, 23
Porphyry, 114
Position of sacred sites, Appendix
Pyrrhus, 171

Rabbinical Law, 48
Rains at Jerusalem, 440
Ramleh, 179, 220
Raymond, grand master of Hospitallers, 289
—— of Plaisance, 134
—— Poitiers, 262
—— Toulouse, 155, 198, 200, 206, 225
Relics, finding of, 126, et passim
Renaud de Chatillon, 288, 289, 291, 339, 371, 380
—— of Sidon, 398
Renegades, story of, at Cyprus, 403
Richard Cœur de Lion, chap. xv., and 404
—— of St. Vitou, 135
—— of Cornwall, 459
Robert of Flanders, 158, 172, 190
—— Normandy, 155, 171
—— Orleans, 130
Roger of Antioch, 230
Russian pilgrims, 475
Rutebeuf, 462
Safiyah bint Hai, 429
Sakhrah, Mohammedan belief concerning, 419
—— purification of, by Saladin, 388
Saladin, 319, 338, 347, 350, 365, chap. xvi.
Saladin’s holy war, 377
Samaritans, 5, 62
Second Crusade, 277
Seif-ed-dín, 358, 404
Selman el Farsí, 427
Sepulchre, Church of the, destroyed by Chosroes, 64;
rebuilt by Modestus, 64;
by Thomas, 93;
destroyed by Hakem, 103
Shakíf, fortress of, 397
Sharafál, 437
Shawer, 301, 311, 313
—— and Dhargam, 301
Sheddád ibn Aus, 427
Shehab-ed-dín, 439
Sherf-ed-dín, 439
Shírkoh, 312
Sicarii, 6
Sigard of Norway, 228
Simon Ben Gioras, chap. ii.
Sophronius, 72
Stephanus, 5
Stephen of Blois, 155, 172, 205
——, Count of Perche, 292
Sufyan eth Thori, 429
Súkel Marifah, 421
Sybille, 337, 339, 367, chap. xiv.
Sylvester converts the Jews, 60

Tancred, 157, 179, 225

Tell es Siyásíyeh, 399
Templars, defeat of, 348
Theodora of Constantinople, 293
Theudas, 4
Thierry of Flanders, 266
Thomas (patriarch) rebuilds Church of Sepulchre, 93
Tiberias, battle of, 350, 378
Tiberius, Alexander, 4
Tithe of Saladin, 363
Titus: his army, 19;
number of, 20, 21;
besieges Jerusalem, chap. ii.
Toghrul Beg, 109
Tomb of David, 436
Tours, Council of, 458
Trajan, revolt under, 49
Tripoli, 226
Truce between Saladin and Richard, 414
True Cross, Invention of, 56;
 discovery of piece of, 195
—— loss of, 381
Tutush, 111
Tyre, 243
—— siege of, 393

Umm el Kheir, 429

Ventidius Cumanus, 4, 5
Vespasian in Galilee, 17;
taxes the Jews, 49

Walter the Penniless, 148

Walter of Cæsarea, 263
William of Cerdagne, 226
Willibald, 123

Yaghmúri, El, 435

Yarmúk, battle of, 69

Zanghi, 253, 262, 265, 270, 272, 330

Zidugdi, 438
Zimisces, 97, 129
Ziráyeh, the, 417

LONDON: PRINTED BY WILLIAM CLOWES AND SONS, STAMFORD STREET

AND CHARING CROSS.
 Transcriber’s Note
The transliteration of Arabic words proved difficult to
render, particularly with respect to multiple diacritical
marks. The printer seemed somewhat undecided about
how best to represent the hamza (ʿ) and ayn (ʾ). For
example, , , or , and
sometimes omitting them (e.g. = ‘Shafiíte’ or
‘Shafiite’ for ‘Shafi‘íte’). They are rendered here as left
and right single quotes. Where the mark is printed atop a
letter, in mid-word, it is inserted to the left. This avoids a
number of unacceptable approximations, e.g., where that
hamza appears atop a Latin i, as in , where
the dot is retained in the italic form used in the text (dái̔ )
The page reference (p. 585) for Saladin’s taking of
Jersulem is incorrect. It has been corrected to p. 385.
Other errors deemed most likely to be the printer’s
have been corrected, and are noted here. The references
are to the page and line in the original. The following
issues should be noted, along with the resolutions.
127.19 for dy[e]ing. Inserted.
138.12 but instead of Replaced.
helping Afsi[s/z]
160.32 occupied by the Added.
caliphat[e] of Cordova
179.9 the time was gone Replaced.
by fo[t/r] negotiation
226.33 The next important Replaced.
place attac[h/k]ed
239.3 allowed to Replaced.
d[e/i]sperse in various
directions
283.19 make themselves Replaced.
masters of the
position[,/.]
331.18 Shaw[a/e], as Replaced.
perfidious as he was
ambitious
343.1 religion, a famil[i]ar Inserted.
thing,
353.14 Guy had taken it Added.
all[.]
383.22 Saladin next Replaced.
attacked Beir[u/ú]t
383.28 While he was at Replaced.
Beir[u/ú]t
389.1 leaving an empty Removed.
space between;[”] Prob.
spurious.
400.2 the Grand Master of Added.
the Templars[,/.]
473.18 called the House of Replaced.
St. Mark[,/.]
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