( They ( ( are ( studying ( ( the behavior ) ( of ( ( quarks , ) ( ( the ( tiny particles ) ) ( that ( ( make up ) ( ( the ( ( protons and ) neutrons ) ) ( that ( reside ( in ( ( the nucleus ) ( of ( the atom ) ) ) ) ) ) ) ) ) ) ) ) ) ) ) . ) )
(ROOT (S (NP (PRP They)) (VP (VBP are) (VP (VBG studying) (NP (NP (DT the) (NN behavior)) (PP (IN of) (NP (NP (NNS quarks)) (, ,) (NP (NP (DT the) (JJ tiny) (NNS particles)) (SBAR (WHNP (WDT that)) (S (VP (VBP make) (PRT (RP up)) (NP (NP (DT the) (NNS protons) (CC and) (NNS neutrons)) (SBAR (WHNP (WDT that)) (S (VP (VB reside) (PP (IN in) (NP (NP (DT the) (NN nucleus)) (PP (IN of) (NP (DT the) (NN atom)))))))))))))))))) (. .)))
They are studying the behavior of quarks, the tiny particles that make up the protons and neutrons that reside in the nucleus of the atom.
(ROOT (S (NP (NNS Protons) (CC and) (NNS neutrons)) (VP (VBP are) (VP (VBN made) (PP (IN of) (NP (NP (NNS quarks)) (, ,) (SBAR (WHNP (WDT which)) (S (VP (VBP are) (NP (NP (JJ fundamental) (NNS particles)) (PP (IN of) (NP (NN matter))))))))))) (. .)))