Implicit Solvent Models for Biomolecular Simulations
Author: BenoƮt Roux
Publisher:
Published: 1999
Total Pages: 217
ISBN-13:
DOWNLOAD EBOOKRead and Download eBook Full
Author: BenoƮt Roux
Publisher:
Published: 1999
Total Pages: 217
ISBN-13:
DOWNLOAD EBOOKAuthor:
Publisher:
Published: 2004
Total Pages: 18
ISBN-13:
DOWNLOAD EBOOKIn this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.
Author: Benoit Roux
Publisher: World Scientific
Published: 2021-08-23
Total Pages: 209
ISBN-13: 9811232776
DOWNLOAD EBOOKThis textbook originated from the course 'Simulation, Modeling, and Computations in Biophysics' that I have taught at the University of Chicago since 2011. The students typically came from a wide range of backgrounds, including biology, physics, chemistry, biochemistry, and mathematics, and the course was intentionally adapted for senior undergraduate students and graduate students. This is not a highly technical book dedicated to specialists. The objective is to provide a broad survey from the physical description of a complex molecular system at the most fundamental level, to the type of phenomenological models commonly used to represent the function of large biological macromolecular machines.The key conceptual elements serving as building blocks in the formulation of different levels of approximations are introduced along the way, aiming to clarify as much as possible how they are interrelated. The only assumption is a basic familiarity with simple mathematics (calculus and integrals, ordinary differential equations, matrix linear algebra, and Fourier-Laplace transforms).
Author: Martin Brieg
Publisher:
Published: 2014
Total Pages:
ISBN-13:
DOWNLOAD EBOOKAuthor: Michael Feig
Publisher: John Wiley & Sons
Published: 2009-12-09
Total Pages: 334
ISBN-13: 3527629262
DOWNLOAD EBOOKA comprehensive view of the current methods for modeling solvent environments with contributions from the leading researchers in the field. Throughout, the emphasis is placed on the application of such models in simulation studies of biological processes, although the coverage is sufficiently broad to extend to other systems as well. As such, this monograph treats a full range of topics, from statistical mechanics-based approaches to popular mean field formalisms, coarse-grained solvent models, more established explicit, fully atomic solvent models, and recent advances in applying ab initio methods for modeling solvent properties.
Author: Michael S. Lee
Publisher:
Published: 2004
Total Pages: 18
ISBN-13:
DOWNLOAD EBOOKIn this work, we design and use a new biomolecular simulation technique that combines explicit solvent molecules and implicit solvent theory. We employ a multigrid approach to speed up the computationally expensive long-range electrostatic energy terms ubiquitous to the classical simulation of biomolecules. It is shown that the multigrid technique affords an order-of-magnitude speedup over conventional cutoff approaches. Our algorithm makes possible a new class of biomolecular simulations that was previously untenable (i.e., the calculation of solvation energies of entire proteins using explicit water molecules). We present comparisons of protein solvation energies obtained from our method and a popular implicit solvent model.
Author: Valerie Daggett
Publisher: Elsevier
Published: 2003-11-26
Total Pages: 477
ISBN-13: 0080493785
DOWNLOAD EBOOKProtein Simulation focuses on predicting how protein will act in vivo. These studies use computer analysis, computer modeling, and statistical probability to predict protein function. * Force Fields* Ligand Binding* Protein Membrane Simulation* Enzyme Dynamics* Protein Folding and unfolding simulations
Author:
Publisher:
Published: 2004
Total Pages: 13
ISBN-13:
DOWNLOAD EBOOKWe present a new hybrid explicit/implicit solvent method for dynamics simulations of macromolecular systems. The method models explicitly the hydration of the solute by either a layer or sphere of water molecules, and the generalized Born (GB) theory is used to treat the bulk continuum solvent outside the explicit simulation volume. To reduce the computational cost, we implemented a multigrid method for evaluating the pairwise electrostatic and GB terms. It is shown that for typical ion and protein simulations our method achieves similar equilibrium and dynamical observables as the conventional particle mesh Ewald (PME) method. Simulation timings are reported, which indicate that the hybrid method is much faster than PME, primarily due to a significant reduction in the number of explicit water molecules required to model hydration effects.
Author: Tamar Schlick
Publisher: Springer Science & Business Media
Published: 2013-04-18
Total Pages: 669
ISBN-13: 0387224645
DOWNLOAD EBOOKVery broad overview of the field intended for an interdisciplinary audience; Lively discussion of current challenges written in a colloquial style; Author is a rising star in this discipline; Suitably accessible for beginners and suitably rigorous for experts; Features extensive four-color illustrations; Appendices featuring homework assignments and reading lists complement the material in the main text
Author: John G. Kirkwood
Publisher: CRC Press
Published: 2001-12
Total Pages: 320
ISBN-13: 9780677010304
DOWNLOAD EBOOK