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This book gives an introduction to molecular biophysics. It starts
from material properties at equilibrium related to polymers,
dielectrics and membranes. Electronic spectra are developed for the
understanding of elementary dynamic processes in photosynthesis
including proton transfer and dynamics of molecular motors. Since
the molecular structures of functional groups of bio-systems were
resolved, it has become feasible to develop a theory based on the
quantum theory and statistical physics with emphasis on the
specifics of the high complexity of bio-systems. This introduction
to molecular aspects of the field focuses on solvable models.
Elementary biological processes provide as special challenge the
presence of partial disorder in the structure which does not
destroy the basic reproducibility of the processes. Apparently the
elementary molecular processes are organized in a way to optimize
the efficiency. Learning from nature by means exploring the
relation between structure and function may even help to build
better artificial solar cells. The reader is exposed to basic
concepts in modern biophysics, such as entropic forces, phase
separation, potential of mean force, electron and proton transfer,
heterogeneous reactions, coherent and incoherent energy transfer as
well as molecular motors. Basic knowledge in classical and Quantum
mechanics, electrostatics and statistical physics is desirable.
Simplified models are presented which can be solved in limited
cases analytically from the guiding lines to generate the basis for
a fundamental understanding of the more complex biophysical
systems. Chapters close with challenging problems whose solutions
are provided at the end of the book to complete the pedagogical
treatment in the book. To the second edition several new chapters
were added. The medium polarization is treated self-consistently
using basic elements of polaron theory and more advanced nonlinear
Schroedinger equations to describe the dynamics of solvation. Ion
transport through a membrane was extended by the discussion of
cooperative effects. Intramolecular transitions are now discussed
in the new edition in much more detail, including also
radiationless transitions. Very recent developments in spectroscopy
are included, especially two-dimensional and hole-burning
spectroscopy. The discussion of charge transfer processes was
extended by including recent results of hole transfer in DNA in
connection with the super-exchange mechanism. The chapter on
molecular motors was rewritten to include the most recent
developments of new models. The book is a useful text for students
and researchers wanting to go through the mathematical derivations
in the theories presented. This book attracts a group of applied
mathematically oriented students and scholars to the exciting field
of molecular biophysics.
Biophysics deals with biological systems, such as proteins, which
ful?ll a va- ety of functions in establishing living systems. While
the biologistuses mostly a phenomenological description, the
physicist tries to ?nd the general c- cepts to classify the
materials and dynamics which underly speci?c processes. The
phenomena span a wide range, from elementary processes, which can
be induced by light excitation of a molecule, to communication of
living s- tems. Thus, di?erent methods are appropriate to describe
these phenomena. From the point of view of the physicist, this may
be Continuum Mechanics to deal with membranes, Hydrodynamics to
deal with transportthrough vessels, Bioinformatics to describe
evolution, Electrostatics to deal with aspects of binding,
Statistical Mechanics to account for temperature and to learn about
the role of the entropy, and last but not least Quantum Mechanics
to und- stand the electronic structure of the molecular systems
involved. As can be seen from the title, Molecular Biophysics, this
book will focus on systems for which su?cient information on the
molecular level is available. Compared to crystallizedstandard
materials studied in solid-state physics, the biological systems
arecharacterizedby verybig unit cells containingproteinswith th-
sands of atoms. In addition, there is always a certain amount of
disorder, so that the systems can be classi?ed as complex.
Surprisingly, the functions like a photocycle or the folding of a
protein are highly reproducible, indicating a paradox situation in
relation to the concept of maximum entropy production.
This textbook presents basic numerical methods and applies them to
a large variety of physical models in multiple computer
experiments. Classical algorithms and more recent methods are
explained. Partial differential equations are treated generally
comparing important methods, and equations of motion are solved by
a large number of simple as well as more sophisticated methods.
Several modern algorithms for quantum wavepacket motion are
compared. The first part of the book discusses the basic numerical
methods, while the second part simulates classical and quantum
systems. Simple but non-trivial examples from a broad range of
physical topics offer readers insights into the numerical treatment
but also the simulated problems. Rotational motion is studied in
detail, as are simple quantum systems. A two-level system in an
external field demonstrates elementary principles from quantum
optics and simulation of a quantum bit. Principles of molecular
dynamics are shown. Modern boundary element methods are presented
in addition to standard methods, and waves and diffusion processes
are simulated comparing the stability and efficiency of different
methods. A large number of computer experiments is provided, which
can be tried out even by readers with no programming skills.
Exercises in the applets complete the pedagogical treatment in the
book. In the third edition Monte Carlo methods and random number
generation have been updated taking recent developments into
account. Krylov-space methods for eigenvalue problems are discussed
in much more detail. Short time Fourier transformation and wavelet
transformation have been included as tools for time-frequency
analysis. Lastly, elementary quantum many-body problems demonstrate
the application of variational and Monte-Carlo methods.
This book gives an introduction to molecular biophysics. It starts
from material properties at equilibrium related to polymers,
dielectrics and membranes. Electronic spectra are developed for the
understanding of elementary dynamic processes in photosynthesis
including proton transfer and dynamics of molecular motors. Since
the molecular structures of functional groups of bio-systems were
resolved, it has become feasible to develop a theory based on the
quantum theory and statistical physics with emphasis on the
specifics of the high complexity of bio-systems. This introduction
to molecular aspects of the field focuses on solvable models.
Elementary biological processes provide as special challenge the
presence of partial disorder in the structure which does not
destroy the basic reproducibility of the processes. Apparently the
elementary molecular processes are organized in a way to optimize
the efficiency. Learning from nature by means exploring the
relation between structure and function may even help to build
better artificial solar cells. The reader is exposed to basic
concepts in modern biophysics, such as entropic forces, phase
separation, potential of mean force, electron and proton transfer,
heterogeneous reactions, coherent and incoherent energy transfer as
well as molecular motors. Basic knowledge in classical and Quantum
mechanics, electrostatics and statistical physics is desirable.
Simplified models are presented which can be solved in limited
cases analytically from the guiding lines to generate the basis for
a fundamental understanding of the more complex biophysical
systems. Chapters close with challenging problems whose solutions
are provided at the end of the book to complete the pedagogical
treatment in the book. To the second edition several new chapters
were added. The medium polarization is treated self-consistently
using basic elements of polaron theory and more advanced nonlinear
Schroedinger equations to describe the dynamics of solvation. Ion
transport through a membrane was extended by the discussion of
cooperative effects. Intramolecular transitions are now discussed
in the new edition in much more detail, including also
radiationless transitions. Very recent developments in spectroscopy
are included, especially two-dimensional and hole-burning
spectroscopy. The discussion of charge transfer processes was
extended by including recent results of hole transfer in DNA in
connection with the super-exchange mechanism. The chapter on
molecular motors was rewritten to include the most recent
developments of new models. The book is a useful text for students
and researchers wanting to go through the mathematical derivations
in the theories presented. This book attracts a group of applied
mathematically oriented students and scholars to the exciting field
of molecular biophysics.
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