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Active transport across the cellular membrane constitutes one of the most fundamental processes of life. Taking advantage of various sources of energy in a cell, e.g., ionic and pH gradients, electrical membrane potential, and ATP hydrolysis, specialized molecular machines known as membrane transporters translocate specific molecular species across the cellular membrane, often against their electrochemical gradients. Elucidation of the molecular mechanisms of these complex machines has long been hampered by lack of sufficient structural information, compounded by the complexity of their mechanisms and the lack of the temporal and spatial resolutions required to study in detail their mechanisms experimentally. Recent advances in structural determination of membrane proteins have resulted in solution of a number of high-resolution structures of membrane transporters setting the stage for simulation studies to investigate various aspects of transport at an atomic level. In this chapter, we report the results of a representative collection of our recent simulation studies performed on a number of membrane transporters for which structures became available recently. The studied transporters are structurally diverse, and, more importantly, function using different mechanisms of energy coupling and structural changes involved in the transport cycle. The studied systems reported in this chapter are: 1) the maltose transporter, representing the superfamily of ABC transporters; 2) the glutamate transporter, a member of the secondary membrane transporter family; 3) glycerol phosphate transporter, representing the major facilitator superfamily; 4) ADP/ATP carrier, a mitochondrial carrier; and, 5) the vitamin B12 transporter, representing outer membrane transporters.