Coarse-Grained Modeling of Biomolecules PDF

FOREWORD

From the prehistoric drawings on the cave walls of Lascaux to the paintings hanging in the Louvre in the late nineteenth century, the visual arts seemed to progress monotonically by adding ever more detail seemingly to give greater realism. A newmovement then exploded near the turn of the twentieth century. Artists began to explore new ways of expressing truths about the visualworld and the visual experience. These newways involved generally more abstract and supercially less detailed techniques than those taught in the art schools. They required no less intellectual discipline, however. The new “modern art,” while not to everyone’s taste, nevertheless, in the opinion of many, brought into existence creations of great beauty and insight.

In recent decades the theoretical study of biomolecules has spawned a similar movement. While acknowledging the power of the highly detailed atomistic models of biomolecular structure and dynamics that can now be simulated using the world’s most powerful computers, the scientists in this movement have been trying to nd new ways of looking at biomolecules and how they move, ways that might be more elegant and ecient. These approaches are oen called “coarse grained” because they employ fewer details in picturing molecules and their motion. The goal of this scientic movement is to nd computationalmodels that still capture the inner truth and, indeed, beauty of life at the molecular level. The new techniques that this task brings forward are no less intellectually demanding nor intriguing than those traditionally used in computer simulation. New ideas ranging from renormalization group theory to neural networks, machine learning and “Big Data” are key to these new developments.

The chapters in this book aim to survey some of the progress in simulating biomolecular dynamics in this new style. The images conjured up by this work are not yet universally loved, but they are beginning to bring new insights into the study of biological structure and function.

The future will decide whether this scienticmovement can bring forth its Picasso or Modigliani.