An engine system, comprising: a) a cylinder; b) an inlet valve configured to control the flow of gases into the cylinder; c) an outlet valve configured to control the flow of gases out of the cylinder; d) a throttle configured to control the flow of fuel into the cylinder; e) a memory including program instructions stored therein; and f1) a processor operably connected to the inlet valve, the outlet valve, the throttle, and the memory, and configured to execute program instructions to f2) control opening/closing of the inlet valve and the outlet valve in accordance with inlet and outlet valve profiles (34, 36) of a Homogeneous Charge Compression Ignition (HCCI) mode and inlet and outlet valve profiles (30, 32) of a Spark Ignition mode; the valve profiles (30, 32, 34, 36) respectively indicating lift of the valves (106, 108) dependent on a crankshaft angle degree and open/close or timing of the inlet and outlet valves; where the HCCI valve profiles (34, 36) in a low valve lift HCCI mode (140, 142) have lower maximum valve lift heights and shorter timing duration than the SI valve profiles (30, 32) in a high valve lift SI mode; and g1) when transitioning from the high valve lift SI mode (136; 146) to the low valve lift HCCI mode (140; 142), a transitional phase of a low valve lift SI mode is achieved, where the processor controls g1.1) the valves (106, 108) lifts into the low valve lift SI mode (138, 144), g1.2) the throttle (112; 176) by moving it from a throttled position to an open position, g1.3) the open/close timings of the valves (106, 108), which are ramped from an SI timing to a lower HCCI timing and spark ignition of the SI mode is delayed whilst a timing of end of fuel injection is delayed after the HCCI mode initiation; g2) thus, delaying activation of a first spark ignition in a first HCCI cycle in the cylinder. a) a cylinder; b) an inlet valve configured to control the flow of gases into the cylinder; c) an outlet valve configured to control the flow of gases out of the cylinder; d) a throttle configured to control the flow of fuel into the cylinder; e) a memory including program instructions stored therein; and f1) a processor operably connected to the inlet valve, the outlet valve, the throttle, and the memory, and configured to execute program instructions to f2) control opening/closing of the inlet valve and the outlet valve in accordance with inlet and outlet valve profiles (34, 36) of a Homogeneous Charge Compression Ignition (HCCI) mode and inlet and outlet valve profiles (30, 32) of a Spark Ignition mode; the valve profiles (30, 32, 34, 36) respectively indicating lift of the valves (106, 108) dependent on a crankshaft angle degree and open/close or timing of the inlet and outlet valves; where the HCCI valve profiles (34, 36) in a low valve lift HCCI mode (140, 142) have lower maximum valve lift heights and shorter timing duration than the SI valve profiles (30, 32) in a high valve lift SI mode; and g1) when transitioning from the high valve lift SI mode (136; 146) to the low valve lift HCCI mode (140; 142), a transitional phase of a low valve lift SI mode is achieved, where the processor controls g1.1) the valves (106, 108) lifts into the low valve lift SI mode (138, 144), g1.2) the throttle (112; 176) by moving it from a throttled position to an open position, g1.3) the open/close timings of the valves (106, 108), which are ramped from an SI timing to a lower HCCI timing and spark ignition of the SI mode is delayed whilst a timing of end of fuel injection is delayed after the HCCI mode initiation; g1.1) the valves (106, 108) lifts into the low valve lift SI mode (138, 144), g1.2) the throttle (112; 176) by moving it from a throttled position to an open position, g1.3) the open/close timings of the valves (106, 108), which are ramped from an SI timing to a lower HCCI timing and spark ignition of the SI mode is delayed whilst a timing of end of fuel injection is delayed after the HCCI mode initiation; g2) thus, delaying activation of a first spark ignition in a first HCCI cycle in the cylinder.