Embark on a fascinating exploration of molecular dynamics, seamlessly blending the new probabilistic interpretation with cutting-edge simulations, some of which are performed on the largest supercomputers on our planet. From fundamental principles to cutting-edge applications, this book offers a rich tapestry of molecular dynamics, and its intersection with biological science, materials science, artificial intelligence, and uncertainty quantification. Beginning with a solid introduction to the intricate world of molecular dynamics, the book goes on to describe the modern probabilistic formulation of molecular dynamics, and ventures into ensemble-based molecular dynamics simulations and free energies, discovering how ensemble techniques revolutionize simulation methodologies and empower researchers to unlock new insights into actionable predictions in real-world problems. Further, the book explores the exciting realm of simulations for advanced materials, and discusses verification, validation and uncertainty quantification, and uncovers the dynamic intersection of molecular dynamics and artificial intelligence illuminating the synergies between these fields and their potential for transformative breakthroughs. Whether you're a seasoned researcher seeking to expand your knowledge or a curious student eager to delve into the complexities of molecular dynamics, this book serves as an indispensable resource, challenging conventional approaches, offering fresh perspectives, and unlocking new insights into real-world problems in this captivating field.