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Biological Physics

Physics -> Biological PhysicsSearch on Amazon

Bioinformatics[1] Biological Networks[6] Biophysics[1]
Cellular Automata[3] Chromatin[1] Membranes[5]
Neurons and Cognition[2] Polymers[11] QM/MM

Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective
Author: Debashish Chowdhury  Language:
A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors transduce input energy into mechanical work. All the . . . . .
Quantum Medicinal Chemistry
Author: Edited by Paolo Carloni and Frank Alber  Language:
Quantum Medicinal Chemistry Contents: Advances in Density-functional-based Modeling Techniques – Recent Extensions of the Car-Parrinello Approach; Density-functional Theory Applications in Computational Medicinal Chemistry; Appl . . . . .
Neocybernetics in Biological Systems
Author: Heikki Hyötyniemi  Language:
Neocybernetics in Biological Systems Concrete examples help to understand complex systems. In this report, the key point is to illustrate the basic mechanisms and properties of neocybernetic system models. Good visualizations are certai . . . . .
Molecular Simulation with Biophysical Applications
Author: Professor Qiang Cui  Language:
Topics: Molecular force field Minimization and normal mode analysis Periodic boundary condition; Ewald summation Molecular Dynamics (NVE;NPT) Monte Carlo (canonical; multicanonical; grandcanonical . . . . .
WHAT IS LIFE - Sub-cellular Physics of Live Matter
Author: Antti J. Niemi  Language:
This is a set of lectures that I presented at the Les Houches 2014 Summer School "Topological Aspects in Condensed Matter Physics". The lectures are an introduction to physics of proteins. To phy . . . . .
Stochastic Models of Evolution in Genetics, Ecology and Linguistics
Author: R. A. Blythe, A. J. McKane  Language:
We give a overview of stochastic models of evolution that have found applications in genetics, ecology and linguistics for an audience of nonspecialists, especially statistical physicists. In particul . . . . .
Optimizations of protein force fields
Author: Yoshitake Sakae, Yuko Okamoto  Language:
In this Chapter we review our works on force fields for molecular simulations of protein systems. We first discuss the functional forms of the force fields and present some extensions of the conventi . . . . .
Introduction to protein folding for physicists
Author: Pablo Echenique  Language:
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved is . . . . .
Simulation in Biology
Author: Jose Rodriguez  Language:
An invitation to simulation is made into a realizable challenge: the reader is taken from scratch to games with words, to mathematical models, to statistical analysis, to simulation of evolution. . . . . .
Random Matrices, the Ulam Problem, Directed Polymers & Growth Models, and Sequence Matching
Author: Satya N. Majumdar  Language:
In these lecture notes I will give a pedagogical introduction to some common aspects of 4 different problems: (i) random matrices (ii) the longest increasing subsequence problem (also known as the Ula . . . . .
A practical guide to stochastic simulations of reaction-diffusion processes
Author: Radek Erban, Jonathan Chapman, Philip Maini  Language:
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative exa . . . . .
Markov-Chain Monte Carlo Methods for Simulations of Biomolecules
Author: Bernd A. Berg  Language:
The computer revolution has been driven by a sustained increase of computational speed of approximately one order of magnitude (a factor of ten) every five years since about 1950. In natural sciences . . . . .
Machines of life: catalogue, stochastic process modeling, probabilistic reverse engineering and the PIs- from Aristotle to Alber
Author: Debashish Chowdhury  Language:
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an en . . . . .
Biological sequence analysis
Author: T. P. Speed  Language:
This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, al . . . . .
Complexity in Biology
Author: Giorgio Parisi  Language:
We will review some of the theoretical progresses that have been in the study of complex systems in physics and of their applications to biology.
Computational Soft Matter: From Synthetic Polymers to Proteins
Author: edited by N. Attig, K. Binder, H. Grubmüller, K. Kremer  Language:
 Computational Soft Matter:  From Synthetic Polymers to Proteins Contents: Introduction to Molecular Dynamics Simulation; Introduction to Monte Carlo Methods; Advanced Simulations for Hydrodynamic Problems: Lattice Boltzmann and Dissipative Particle Dynamics; Monte . . . . .
Multiscale Simulation Methods in Molecular Sciences
Author: Johannes Grotendorst Norbert Attig Stefan Blügel Dominik Marx  Language:
Multiscale Simulation Methods in Molecular Sciences Contents: Methodological Foundations; Multiscale Simulation Methods for Solids and Materials; Multiscale Simulation Methods for Soft Matter and Biological Systems; Numerical Methods and Parallel Co . . . . .

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