The further reduction of greenhouse gas emissions is essential for climate neutral aviation to accommodate the expected increase in air travel and at the same time to pursue its service to society and environment. This calls for rapid introduction of advanced and disruptive technological solutions for airframe, propulsion and energy carriers, well beyond the continuous improvements of the past decades that have led to the state-of-the-art aircraft technologies. Many technology investigations have therefore recently been made in various directions, including innovative airframe concepts (e.g. as presented in [1]), advanced propulsion concepts (e.g. as presented in [2]) and carbon-free energy carrier concepts (e.g. as presented in [3]). For design, analysis and evaluation of such novel concepts, fast, flexible and efficient modelling tools are required. Moreover, multi-disciplinary modelling and optimization are required to incorporate the most appropriate technologies and to identify the most promising design solutions. NLR is active in this area in various state-of-the-art research and development projects in which these tools for multi-disciplinary modelling and optimization are developed, as well as deployed in advanced aircraft design use-cases. For example, in the Clean Sky 2 (CS2) project NOVAIR [4] the design of aircraft configurations for hybrid-electric-propulsion (HEP) has been investigated. Collaborative multi-disciplinary modelling and optimization methodologies and tools are pursued in the ongoing Horizon2020 (H2020) project AGILE4.0 [5]. In the ongoing H2020 project IMOTHEP [6], HEP system design for conservative and radical aircraft configuration concepts are under investigation. This paper presents a brief overview of the recent developments in the mentioned areas. Among others, the efficient modelling and quick evaluation of the overall aircraft emissions are essential for the assessment of the greenhouse gas effects of novel aircraft and propulsion concepts. This requires adequate representation of the aircraft-level behaviour including engine and propulsion aspects and considering flight mission and exhaust emissions details. The main methodologies and tools that are used in these analyses will be addressed and some typical results will be shown.