2013 Chemistry Nobel Prize Resources



Martin Karplus        Michael Levitt         Arieh Warshel

» Overview
» Quote from John Haynes, CEO of AIP Publishing
» The Journal of Chemical Physics and Proceedings articles by the Chemistry Laureates (Free Access)
» Quote from Marsha I. Lester, JCP Editor-in-Chief
» Quote from James L. Skinner, JCP Associate Editor
» Quote from John E. Straub, JCP Associate Editor
» Quote from Dave Thirumalai, JCP Guest Editor of the Special Topic: Chemical Physics of Biological Systems
» From Physics Today
» Listen to Martin Gruebele and D. Thirumalai on "Reaches of Chemical Physics in Biology"
» Biographies and personal pages
» Press release

Overview

The work behind this year's Nobel Prize in Chemistry focuses on how to answer questions about the function of large complex molecular systems such as those involved in photosynthesis and human vision. In modern biological physics, laboratory experiments are run side-by-side with computational modeling, the two relying heavily on each other to reveal in the end why a particular system behaves the way it does. Multiscale modeling explains properties and behavior of large systems, such as complex biomolecules, by focusing on important details, such as key sites on the biomolecules where chemical reactions take place. The foundational work in multiscale modeling was done by the three laureates — Karplus, Levitt, and Warshel — and it helps to accurately explain and predict how important behaviors involving electrons at the atomic and molecular level contribute to function at the systems level.

In the 1970s Warshel and Karplus began collaborating on this multiscale modeling technique, relying on each other's area of expertise to devise a computer program to describe complex chemical systems that would combine the approaches of classical physics — in which atoms are treated as colliding billiard balls — and quantum mechanics — in which electrons are modeled as being in a cloud of possible positions. Levitt and Warshel then made further important strides which made it possible to study even larger systems such as proteins. Understanding protein function and their subsequent degradation can lead to insights into a number of diseases such as Alzheimer's.

Quote from John Haynes, CEO of AIP Publishing

“Today's Nobel Prize announcement is a great example of how the study of Physics, Chemistry and Biology are crossing traditional boundaries to help tackle tough problems ranging from designing new materials for renewable energy to pharmaceutical drug design.”

The Journal of Chemical Physics and Proceedings Articles by the Chemistry Laureates (Free Access)

AIP Journal and Proceedings Articles by Martin Karplus Related to Complex and Biological Systems

AIP journal content written by the 2013 Nobel Laureates in Chemistry is free until December 31, 2013.

Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method
Guishan Zheng, Anders M. N. Niklasson, and Martin Karplus
J. Chem. Phys. 135, 044122 (2011)

Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI
Victor Ovchinnikov, Martin Karplus, and Eric Vanden-Eijnden
J. Chem. Phys. 134, 085103 (2011)

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise
Paul Maragakis, Felix Ritort, Carlos Bustamante, Martin Karplus, and Gavin E. Crooks
J. Chem. Phys. 129, 024102 (2008)

Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations
Arjan van der Vaart and Martin Karplus
J. Chem. Phys. 126, 164106 (2007)

Conformational sampling via a self-regulating effective energy surface
Ryan Bitetti-Putzer, Aaron R. Dinner, Wei Yang, and Martin Karplus
J. Chem. Phys. 124, 174901 (2006)

Simulation of conformational transitions by the restricted perturbation–targeted molecular dynamics method
Arjan van der Vaart and Martin Karplus
J. Chem. Phys. 122, 114903 (2005)

Calculation of the aqueous solvation energy and entropy, as well as free energy, of simple polar solutes
Shunzhou Wan, Roland H. Stote, and Martin Karplus
J. Chem. Phys. 121, 9539 (2004)

Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials
Wei Yang, Ryan Bitetti-Putzer, and Martin Karplus
J. Chem. Phys. 120, 9450 (2004)

Free energy simulations: Use of reverse cumulative averaging to determine the equilibrated region and the time required for convergence
Wei Yang, Ryan Bitetti-Putzer, and Martin Karplus
J. Chem. Phys. 120, 2618 (2004)

Self-guided enhanced sampling methods for thermodynamic averages
Ioan Andricioaei, Aaron R. Dinner, and Martin Karplus
J. Chem. Phys. 118, 1074 (2003)

See more JCP articles by Martin Karplus »

JCP articles published by Arieh Warshel related to complex systems

AIP journal content written by the 2013 Nobel Laureates in Chemistry is free until December 31, 2013.

The surface constraint all atom model provides size independent results in calculations of hydration free energies
Yuk Yin Sham and Arieh Warshel
J. Chem. Phys. 109, 7940 (1998)

A stringent test of the cavity concept in continuum dielectrics
Arno Papazyan and Arieh Warshel
J. Chem. Phys. 107, 7975 (1997)

Quantum-mechanical calculations of solvation free energies. A combined ab initio pseudopotential free-energy perturbation approach
Nagarajan Vaidehi, Tomasz Adam Wesolowski, and Arieh Warshel
J. Chem. Phys. 97, 4264 (1992)

A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations
Frederick S. Lee and Arieh Warshel
J. Chem. Phys. 97, 3100 (1992)

Microscopic simulations of macroscopic dielectric constants of solvated proteins
Gregory King, Frederick S. Lee, and Arieh Warshel
J. Chem. Phys. 95, 4366 (1991)

Investigation of the free energy functions for electron transfer reactions
Gregory King and Arieh Warshel
J. Chem. Phys. 93, 8682 (1990)

Quantum corrections for rate constants of diabatic and adiabatic reactions in solutions
A. Warshel and Z. T. Chu
J. Chem. Phys. 93, 4003 (1990)

A surface constrained all-atom solvent model for effective simulations of polar solutions
Gregory King and Arieh Warshel
J. Chem. Phys. 91, 3647 (1989)

The extended Ewald method: A general treatment of long-range electrostatic interactions in microscopic simulations
Satoru Kuwajima and Arieh Warshel
J. Chem. Phys. 89, 3751 (1988)

Effects of solute–solvent coupling and solvent saturation on solvation dynamics of charge transfer reactions
J.-K. Hwang, S. Creighton, G. King, D. Whitney, and A. Warshel
J. Chem. Phys. 89, 859 (1988)

See more JCP articles by Arieh Warshel »

Quote from Marsha I. Lester, JCP Editor-in-Chief

“Many of the seminal papers by the Nobel Laureates reporting the first ways to embed quantum dynamics with classical simulations were published in the Journal of Chemical Physics. Martin Karplus, in particular, has published much of his science (over 160 papers!) in the Journal of Chemical Physics and this work has been cited nearly 20,000 times. This field continues to be a key focus for the Journal, which just this year published a Perspective article on ‘Reaches of Chemical Physics in Biology’ by Martin Gruebele and Dave Thirumalai and a Special Topic collection of papers on ‘Chemical Physics of Biological Systems’ in the 28 Sept 2013 issue of the Journal of Chemical Physics.”

Quote from James L. Skinner, JCP Associate Editor

“I think this is a wonderful chemistry Nobel — one that is very exciting to those of us in the fields of molecular simulation and theoretical chemistry. Molecular simulation by computer has become an extremely useful tool for studying structure, dynamics, mechanism, and function of complex systems, from biology to materials science and energy technology. The marriage of classical and quantum mechanics in implementing the simulation, as highlighted in this year's prize announcement, is especially powerful. The awarding of the prize to Karplus, Levitt, and Warshel is very well deserved indeed, and brings enhanced visibility to the increasingly important method of molecular simulation.”

Quote from John E. Straub, JCP Associate Editor

“The seminal work of Karplus, Levitt, and Warshel led to the creation of a new paradigm for addressing complex problems in chemistry. Before the advent of multiscale modeling, the primary approach to addressing questions in chemistry was through experiment and the application of theory. The development of computational models created a new paradigm for solving problems in chemistry, a 'third way' that stands between theory and experiment. The fundamental principles of physics and chemistry are used to create 'in silico' representations of systems that can be interrogated at a level of detail that cannot be approached by experiment or captured by a single theory. Complex problems in chemical, biological, materials, and energy science are now routinely approached using a synergistic combination of theory, computational modeling, and experiment. The recent JCP Perspective 'Reaches of Chemical Physics in Biology' and the associated Special Issue 'Chemical Physics of Biological Systems' provide beautiful examples of how this modern approach can be used to address fundamental problems in biology.”

Quote from Dave Thirumalai, JCP Guest Editor of the Special Topic: Chemical Physics of Biological Systems

“The pioneering works of these three scientists showed how computer simulations are a powerful of solving major problems in many complex systems. In particular, their works have helped us understand many intricate biological processes ranging from enzyme kinetics and have provided insights into how molecular forces modulate functions of biological machines. In addition, these methods are indispensable for obtaining refined structures of complex biological systems from electron density maps generated using X-ray and cryo EM methods. It is also likely that the validation of computer simulation approaches by this wonderful recognition will pave the way for the works of other scientists to be considered for publication in prestigious journals without the current prejudice. Thus, not only do they deserve this recognition it also will have the added benefit for the community at large.”

From Physics Today

Molecular Dynamics Simulations of Proteins
Martin Karplus
Physics Today 40, October, 68 (1987)

Listen to Martin Gruebele and D. Thirumalai on "Reaches of Chemical Physics in Biology"

gruebele thumalai podcast

In this Perspective, part of the special topic section on chemical physics of biological systems, the authors consider a wide range of contributions, all the way from the molecular level, to molecular assemblies, chemical physics of the cell, and finally systems-level approaches, based on the contributions to this special issue. Chemical physicists can look forward to an exciting future where computational tools, analytical models, and new instrumentation will push the boundaries of biological inquiry. Read the Perspective.

Biographies and personal pages

Biographies
Martin Karplus
Michael Levitt
Arieh Warshel

Websites
Karplus's Research Page
Levitt's Research Page
Warshel's Research Page

Press release

more 2013 Nobel Prize in Chemistry highlights the cross-disciplinary nature of today’s research environment (10/9/13)