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This chapter focuses on metadynamics, which was first introduced in 2002 and then improved with several variants in the past decade. It provides an introduction to the basic concepts of molecular dynamics and of free‐energy calculations. When appropriate collective variables (CVs) are used, the free‐energy landscape provides a quantitative picture of the transition in terms of reactants and products...
This chapter focuses on the recent developments in different polarizable force fields. These include atomic multipole optimized energetics for biomolecular applications (AMOEBA), sum of interactions between fragments ab initio computed (SIBFA), nonempirical molecular orbital (NEMO), CHARMM fluctuating charge model (FQ), and polarizable protein force field (PFF). The chapter begins with a brief introduction...
This chapter gives an introduction to protein simulation methodology aimed at experimentalists and graduate students new to in silico investigations. More emphasis is placed on the knowledge needed to select appropriate simulation protocols, leaving theoretical and mathematical depth for other texts to take care of. The chapter explains some of the more practical considerations of performing simulations...
Proteins specifically interact with other proteins and nucleic acids to form a wide variety of assemblies, from binary complexes to the elaborate multicomponent machines that perform many of the cellular functions. This chapter describes how Critical Assessment of PRedicted Interactions (CAPRI) is organized, summarizes the results of protein‐protein recognition, and shows how CAPRI has fostered progress...
The kinetic Monte Carlo (KMC) method has found applications in several broad areas of science and engineering, with many modeling studies of surface deposition processes, heterogeneous catalysis, and now in electrochemical systems. One of the fundamental challenges in applying KMC to electrochemical systems is the treatment of charges, including the calculation of dynamic electric fields, which affect...
This chapter discusses the computational tools that were developed to specifically address liquid interfacial systems. It summarizes the microscopic insight gained about the structure and dynamics of neat liquid interfaces and the behavior of solute molecules adsorbed at these interfaces. The chapter focuses on molecular‐level information that in recent years has been compared directly with experiments...
This chapter focuses on the molecular aspect, particularly, on the application of different computational methods to investigate structural and thermodynamic stability, guest and lattice dynamics, thermal transport and mechanisms for homogeneous and heterogeneous crystallization. A general and elegant model to predict the thermodynamic stability of clathrate compounds and, in particular, for gas hydrates,...
This chapter discusses excited electronic states of anions that possess enough energy to access an electronic continuum, or in other words, excited states where the excitation energy is greater than the electron detachment energy. Such states exist only as temporary, “auto‐ionizing” resonances. The chapter provides a discussion of the basic quantum mechanical concepts that underlie the collection...
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