Environmental health awareness has elevated in recent years alongside the evidence that supports the need to mitigate harmful greenhouse gas (GHG) emissions from non-renewable energy resources. The transportation sector alone significantly contributes to the pollutants on a global scale. Although it is commonly used for its superior energy-density and fuel efficiency, diesel engines are a significant portion of the transportation sector that contributes to these pollutants. As a result, this motivates novel research to simultaneously drive fuel efficiency improvements and emissions reductions. The aftertreatment system for a diesel engine is critical in reducing the amount of harmful tailpipe emissions. Efficient operation of these aftertreatment systems generally requires elevated temperatures of 250◦C or above. In this effort, a flexible valvetrain will be utilized to demonstrate fuel-efficient strategies via intake valve closure (IVC) modulation at elevated speeds and loads. In addition, thermal management strategies will be demonstrated at low-to-moderate loads via cylinder deactivation (CDA), cylinder cutout, exhaust valve opening (EVO) modulation, and high-speed idle operation.At elevated engine speeds, late intake valve closure (LIVC) enables improved cylinder filling via a dynamic charging effect. It is experimentally and analytically demonstrated that LIVC at 2200 RPM and 7.6 bar to 12.7 bar BMEP can be used to increase the volumetric efficiency and enable higher exhaust gas recirculation fractions without penalizing the air-to-fuel ratio. As a result, efficiency improving injection advances are implemented to achieve 1.2% and 1.9% fuel savings without sacrificing NOx penalties. In order to implement the LIVC benefits on a cammed engine, production-viable valve profile solutions were investigated. It is demonstrated that lost-motion-enabled and/or added-motion-enabled boot shape profiles are capable of improving volumetric efficiency at elevated engine speeds and loads. These profiles were also considered for one (of two) -valve modulation and two-valve modulation. Nearly 95% of the volumetric efficiency benefits are possible using production-viable boot or phase profiles, while 80% of the benefits are possible for single-valve modulation. At curb idle, CDA and cylinder cutout operation realize stay-warm aftertreatment thermal management improvements by leveraging their impact on the gas exchange process. Specifically, cylinder cutout demonstrates 17% fuel savings, while CDA demonstrates 40% fuel savings, over the conventional six-cylinder thermal calibration. Additionally, the performance of cylinder cutout is subject to the geometry of the exhaust manifold, location of the EGR loop, and ability to control the exhaust manifold pressure. Elevating the idle speed, while maintaining the same idle load, enables improved aftertreatment warm-up performance with engine-out NOx and PM levels no higher than a state-of-the-art thermal calibration at conventional idle operation. Elevated idle speeds of 1000RPM and 1200 RPM, compared to conventional idle at 800 RPM, realized 31% to 51% increase in exhaust flow and 25◦C to 40◦C increase in engine-out temperature, respectively. Additional engine-out temperature benefits are experimentally demonstrated at all three idle speeds considered (800, 1000, and 1200 RPM), without compromising the exhaust flow rates or emissions, by modulating the EVO timing. At low-to-moderate loads modern diesel engines manipulate exhaust manifold pressures to drive EGR and thermally manage the aftertreatment. In these engines exhaust manifold pressure control is typically achieved via either a valve after the turbine, a variable geometry turbine, or wastegating. It is experimentally demonstrated that valvetrain flexibility enables efficient engine and aftertreatment operation without requiring exhaust manifold pressure control. Specifically, IVC modulation and CDA at elevated engine speeds, along with EVO modulation, CDA, and internal EGR at low engine speeds can match, or improve, efficiency and thermal management performance compared to a stock thermal calibration that requires exhaust manifold pressure control.