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Embark on a fascinating exploration of molecular dynamics, which combines the authors' new probabilistic interpretation with cutting-edge simulations, some of which are performed on the largest supercomputers on our planet. From fundamental principles to innovative applications, this book covers the rich tapestry of molecular dynamics and its intersections with biological and medical sciences, materials science and engineering, and artificial intelligence, alongside uncertainty quantification. This enables the authors to highlight the critical role of molecular dynamics in delivering actionable outcomes for drug discovery, materials design and beyond. Beginning with a solid introduction to the intricate world of molecular dynamics, the book goes on to describe its modern probabilistic formulation. It investigates ensemble-based molecular dynamics simulations and free energies, uncovering both the way that ensemble techniques revolutionize simulation methodologies and how they empower researchers to generate new insights. Further, the book explores the exciting realm of simulations for advanced materials and discusses verification, validation and uncertainty quantification, illuminating the synergies between molecular dynamics and artificial intelligence and their potential for transformative breakthroughs. Whether you are a seasoned researcher seeking to expand your knowledge or a curious student eager to investigate 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.