In science, matter is anything that has mass. [1] All matter is made up of atoms, which in turn are made up of elementary particles. Of the set of elementary particles, fermions, particles with 1/2 integer spin, are considered as the "matter" portion of the universe, whereas bosons, particles with integer spin, are considered as the "energy" portion of the universe. [2] In thermodynamics, whenever matter crosses the boundary of a system, its effect on the system is quantified by how it changes the internal energy of the system, generally measured by changes in chemical potential. [3]

References
1. Clark, John O.E. (2004). The Essential Dictionary of Science, (pg. 356). New York: Barnes & Noble Books.
2. Veltmann, Martinus. (2003). Facts and Mysteries in Elementary Particle Physics. New Jersey: World Scientific.
3. Daintith, John. (2004). Oxford Dictionary of Chemistry, (pg. 125). New York: Oxford University Press.