Simulation in Force Spectroscopy

Simulation has played an important role in the study of molecular-scale forces since the 1970s, almost from the time such forces could first be measured experimentally. Over the past three decades, as experimental probes have grown in sophistication and sensitivity, the scope and accuracy of computer modeling have developed in step. Today simulation and experiment are so closely linked in the field of force spectroscopy that it seems hardly possible to consider one without the other. Although the influence of simulation is certainly growing, with some notable exceptions the frontier has to this point been driven largely by experiment. In comparison to pencil-and-paper theory, which has been extremely successful in helping to define unifying concepts and analytical frameworks, the principle contribution of computation has been to fill in missing details, and to clarify and help explain experimental findings. This role is beginning to change, however, as steady advances in methodology and computer hardware expand the versatility and reliability of modeling approaches, and improving software makes it increasingly feasible for scientists without backgrounds in simulation to adopt these techniques in their own research.1 Modeling is becoming both increasingly predictive, and increasingly accessible. Another emerging role for simulation in the field of force spectroscopy is to investigate questions experiments cannot address, such as the study of phenomena occurring on very short time and length scales, atomic-scale structure or energy flow, and the distribution of forces among simultaneously interacting contacts. A simple example occurs in the study of force-separation curves. In an experiment, mechanical instability in the transducer may prevent portions of the force spectrum from being measured, or limit sensitivity by requiring a stiffer spring constant. In a simulation however, where forces can be applied in any arbitrary way, or parts held fixed at arbitrary positions, one can study scenarios which may not be achievable by experiment, even in principle. As we will see throughout, this powerful advantage has been used in a number of studies to shed light on phenomena that might have otherwise gone unrecognized, or worse, been misinterpreted. This chapter aims to provide an introduction to the role of simulation in force spectroscopy. I survey the most important computational techniques, including a discussion of their strengths and weaknesses. Particular attention is given to the difference in timescales probed by experiments and simulation, and the consequences this has for comparing results from the two approaches. The chapter concludes with a discussion of some selected case studies, 6