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An engine and a method of operating an engine. One method includes: routing air to both a donor and a non-donor cylinder of an engine; combusting an air fuel mixture in the cylinders; routing exhaust gas from the non-donor cylinder through an exhaust manifold; and recirculating exhaust gas from the

An engine and a method of operating an engine. One method includes: routing air to both a donor and a non-donor cylinder of an engine; combusting an air fuel mixture in the cylinders; routing exhaust gas from the non-donor cylinder through an exhaust manifold; and recirculating exhaust gas from the donor cylinder through an aftertreatment system and a cooler back to the intake manifold. Another method includes: recirculating exhaust gas from a first cylinder of an engine to an intake stream or air-fuel mixture of the engine, whereby: the recirculated exhaust gas from the first cylinder flows through an after treatment system; and the recirculated exhaust gas is cooled to a lower temperature after the after treatment system; and routing exhaust gas from the second cylinder through an exhaust manifold.

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1. A method comprising: flowing exhaust gas from a first cylinder of a reciprocating engine through an after treatment system;cooling the exhaust gas after the after treatment system;recirculating the exhaust gas from the first cylinder to an intake stream or air-fuel mixture of the first cylinder a

1. A method comprising: flowing exhaust gas from a first cylinder of a reciprocating engine through an after treatment system;cooling the exhaust gas after the after treatment system;recirculating the exhaust gas from the first cylinder to an intake stream or air-fuel mixture of the first cylinder and a second cylinder of the reciprocating engine;routing at least a portion of the exhaust gas from the second cylinder through a first turbine;compressing the intake stream or air-fuel mixture to the first cylinder and the second cylinder with a compressor, wherein the compressor is operatively attached to at least one of the first turbine or a second turbine;directly injecting at least one fuel directly into one of the first cylinder and the second cylinder;retarding an injection timing of the first cylinder; andadvancing an injection timing of the second cylinder. 2. The method of claim 1 wherein the reciprocating engine operates on diesel fuel. 3. The method of claim 1, wherein the reciprocating engine operates on gasoline fuel. 4. The method of claim 1, wherein the reciprocating engine operates on one of natural gas fuel, syngas, landfill gas, a CO/H2 mixture, methanol, ethanol, a single component alcohol, blended alcohol, and combinations thereof. 5. The method of claim 1 wherein the reciprocating engine operates on a plurality of fuels. 6. The method of claim 5, wherein the plurality of fuels comprise diesel and one of natural gas and ethanol. 7. The method of claim 1, further comprising providing the first reciprocating cylinder with an air fuel mixture having a first air/fuel ratio and providing the second reciprocating cylinder with an air fuel mixture having a second air/fuel ratio, wherein the first air/fuel ratio is less than the second air/fuel ratio. 8. The method of claim 1, wherein the after treatment system comprises one of a diesel particulate filter, a diesel oxidation catalyst, a flow-through filter, a three-way catalyst, and a selective catalytic reduction catalyst. 9. The method of claim 1, further comprising: increasing an amount of fuel supplied to the first cylinder; anddecreasing an amount of fuel supplied to the second cylinder, so as to maintain a predetermined power output from the reciprocating engine. 10. An engine comprising: a first reciprocating cylinder;a second reciprocating cylinder;an exhaust manifold, configured to provide an egress path for exhaust emissions from the first reciprocating cylinder and the second reciprocating cylinder;an intake manifold, configured to provide an input path for an air fuel mixture to the first reciprocating cylinder and the second reciprocating cylinder;an exhaust gas recirculating (EGR) subsystem comprising: an after treatment system; andan EGR cooler in series with said after treatment system, wherein the EGR subsystem routes exhaust emissions from the first reciprocating cylinder back to the intake manifold; anda direct injection means, configured to directly inject at least one fuel into one of the first cylinder and the second cylinder, further wherein at least one of: an injection timing of the first cylinder is retarded as compared to an injection timing of the second cylinder; andan injection timing of the second cylinder is advanced as compared to an injection timing of the first cylinder. 11. The engine of claim 10, wherein the first reciprocating cylinder receives an air fuel mixture having a first air/fuel ratio and the second reciprocating cylinder receives an air fuel mixture having a second air/fuel ratio, wherein the first air/fuel ratio is less than the second air/fuel ratio. 12. The engine of claim 10, wherein the after treatment system comprises one of a diesel particulate filter, a diesel oxidation catalyst, a flow-through filter, a three-way catalyst, and a selective catalytic reduction catalyst. 13. The engine of claim 10, further comprising a turbocharger, the turbocharger comprising a turbine operatively attached to a compressor, wherein the exhaust emissions from the second reciprocating cylinder is routed to the turbine, and compressed intake air from the compressor is routed to the intake manifold. 14. The engine of claim 10, wherein the engine operates on diesel fuel. 15. The engine of claim 10, wherein the engine operates on gasoline fuel. 16. The engine of claim 10, wherein the engine operates on one of natural gas fuel, syngas, landfill gas, a CO/H2 mixture, methanol, ethanol, a single component alcohol, blended alcohol, and combinations thereof. 17. The engine of claim 10, wherein the engine operates on a plurality of fuels. 18. The engine of claim 17, wherein the plurality of fuels comprise diesel and one of natural gas and ethanol. 19. The engine of claim 10, further wherein an amount of fuel supplied to the first cylinder is greater than an amount of fuel supplied to the second cylinder. 20. A method comprising: routing air to a donor cylinder and a non-donor cylinder of a reciprocating engine;combusting an air fuel mixture in the donor cylinder and the non-donor cylinder;routing exhaust gas from the non-donor cylinder through an exhaust manifold;recirculating exhaust gas from the donor cylinder through an aftertreatment system and a cooler back to the intake manifold of the donor cylinder and the non-donor cylinder;directly injecting at least one fuel directly into one of the first cylinder and the second cylinder;retarding an injection timing of the first cylinder; andadvancing an injection timing of the second cylinder. 21. The method of claim 20, wherein the reciprocating engine operates on diesel fuel. 22. The method of claim 20, wherein the reciprocating engine operates on gasoline fuel. 23. The method of claim 20, wherein the reciprocating engine operates on one of natural gas fuel, syngas, landfill gas, a CO/H2 mixture, methanol, ethanol, a single component alcohol, blended alcohol, and combinations thereof. 24. The method of claim 20, wherein the reciprocating engine operates on a plurality of fuels. 25. The method of claim 24, wherein the plurality of fuels comprise diesel and one of natural gas and ethanol. 26. The method of claim 20, further comprising providing the first reciprocating cylinder with an air fuel mixture having a first air/fuel ratio and providing the second reciprocating cylinder with an air fuel mixture having a second air/fuel ratio, wherein the first air/fuel ratio is less than the second air/fuel ratio. 27. The method of claim 20, wherein the after treatment system comprises one of a diesel particulate filter, a diesel oxidation catalyst, a flow-through filter, a three-way catalyst, and a selective catalytic reduction catalyst. 28. The method of claim 20, further comprising: increasing an amount of fuel supplied to the first cylinder; anddecreasing an amount of fuel supplied to the second cylinder, so as to maintain a predetermined power output from the reciprocating engine. 29. A method comprising: recirculating exhaust gas from a first cylinder of a reciprocating engine to an intake stream or air-fuel mixture of the first cylinder and a second cylinder of the reciprocating engine, whereby: the recirculated exhaust gas from the first cylinder flows through an after treatment system; andthe recirculated exhaust gas is cooled to a lower temperature after the after treatment system;routing exhaust gas from the second cylinder through an exhaust manifold;directly injecting at least one fuel directly into one of the first cylinder and the second cylinder; and one of:retarding an injection timing of the first cylinder; andadvancing an injection timing of the second cylinder. 30. The method of claim 29, wherein the reciprocating engine operates on diesel fuel. 31. The method of claim 29, wherein the reciprocating engine operates on gasoline fuel. 32. The method of claim 29, wherein the reciprocating engine operates on one of natural gas fuel, syngas, landfill gas, a CO/H2 mixture, methanol, ethanol, a single component alcohol, blended alcohol, and combinations thereof. 33. The method of claim 29, wherein the reciprocating engine operates on a plurality of fuels. 34. The method of claim 33, wherein the plurality of fuels comprise diesel and one of natural gas and ethanol. 35. The method of claim 29, further comprising providing the first cylinder with an air fuel mixture having a first air/fuel ratio and providing the second cylinder with an air fuel mixture having a second air/fuel ratio, wherein the first air/fuel ratio is less than the second air/fuel ratio. 36. The method of claim 29, wherein the after treatment system comprises one of a diesel particulate filter, a diesel oxidation catalyst, a flow-through filter, a three-way catalyst, and a selective catalytic reduction catalyst. 37. The method of claim 29, further comprising: increasing an amount of fuel supplied to the first cylinder; anddecreasing an amount of fuel supplied to the second cylinder, so as to maintain a predetermined power output from the reciprocating engine. 38. A method comprising: flowing recirculating exhaust gas from a first cylinder of a reciprocating engine through an after treatment system;cooling the recirculating exhaust gas after the after treatment system, wherein the after treatment system comprises one of a diesel particulate filter, a diesel oxidation catalyst, a flow-through filter, a three-way catalyst, and a selective catalytic reduction catalyst;recirculating exhaust gas from a first cylinder of the reciprocating engine to a compressor;routing exhaust gas from the second cylinder through a turbine;compressing the intake stream or air-fuel mixture to the first cylinder and the second cylinder and the recirculating exhaust gas with a compressor, wherein the compressor is operatively attached to the turbine;directly injecting at least one fuel directly into one of the first cylinder and the second cylinder; and one of:retarding an injection timing of the first cylinder; andadvancing an injection timing of the second cylinder. 39. The method of claim 38, wherein the reciprocating engine operates on diesel fuel. 40. The method of claim 38, wherein the reciprocating engine operates on gasoline fuel. 41. The method of claim 38, wherein the reciprocating engine operates on one of natural gas fuel, syngas, landfill gas, a CO/H2 mixture, methanol, ethanol, a single component alcohol, blended alcohol, and combinations thereof. 42. The method of claim 38, wherein the reciprocating engine operates on a plurality of fuels. 43. The method of claim 42, wherein the plurality of fuels comprise diesel and one of natural gas and ethanol. 44. The method of claim 38, further comprising providing the first cylinder with an air fuel mixture having a first air/fuel ratio and providing the second cylinder with an air fuel mixture having a second air/fuel ratio, wherein the first air/fuel ratio is less than the second air/fuel ratio. 45. The method of claim 38, further comprising: increasing an amount of fuel supplied to the first cylinder; anddecreasing an amount of fuel supplied to the second cylinder, so as to maintain a predetermined power output from the reciprocating engine. 46. A method comprising: recirculating exhaust gas from a first cylinder of a reciprocating engine back to the reciprocating engine;flowing the recirculating exhaust gas through an after treatment system and a first turbine;cooling the recirculating exhaust gas after the first turbine;compressing the recirculating exhaust gas after the cooling with a first compressor, wherein the first compressor is operatively attached to the first turbine;recirculating the compressed recirculating exhaust gas to the intake stream or air-fuel mixture to the first cylinder and the second cylinder;routing exhaust gas from the second cylinder through a second turbine; andcompressing the intake stream or air-fuel mixture of the second cylinder with a second compressor, wherein the compressor is operatively attached to the second turbine. 47. The method of claim 46, wherein the reciprocating engine operates on diesel fuel. 48. The method of claim 46, wherein the reciprocating engine operates on gasoline fuel. 49. The method of claim 46, wherein the reciprocating engine operates on one of natural gas fuel, syngas, landfill gas, a CO/H2 mixture, methanol, ethanol, a single component alcohol, blended alcohol, and combinations thereof. 50. The method of claim 46, wherein the reciprocating engine operates on a plurality of fuels. 51. The method of claim 50, wherein the plurality of fuels comprise diesel and one of natural gas and ethanol. 52. The method of claim 46, further comprising providing the first cylinder with an air fuel mixture having a first air/fuel ratio and providing the second cylinder with an air fuel mixture having a second air/fuel ratio, wherein the first air/fuel ratio is less than the second air/fuel ratio. 53. The method of claim 46, wherein the after treatment system comprises one of a diesel particulate filter, a diesel oxidation catalyst, a flow-through filter, a three-way catalyst, and a selective catalytic reduction catalyst. 54. The method of claim 53, further comprising directly injecting at least one fuel directly into one of the first cylinder and the second cylinder. 55. The method of claim 54, further comprising one of: retarding an injection timing of the first cylinder; andadvancing an injection timing of the second cylinder. 56. The method of claim 55, further comprising: increasing an amount of fuel supplied to the first cylinder; anddecreasing an amount of fuel supplied to the second cylinder, so as to maintain a predetermined power output from the reciprocating engine.