U Ba Khin and his reference to Parajikan Atthakatha U Ba Khin, in IMC: Personal Experiences of Candidates, writes some quite interesting "explanatory remarks" about the experiences that Mr. J. Van Amersfoort had during a meditation course. 

In those remarks U Ba Khin sees the Parajikan Atthakatha as an authoritative treatise which talks about the "realization of the Truth by an analysis of the kalapas in the body with the lens of Samadhi obtained through Anapana Sati". 

I was not able to find the text of that Parajikan Atthakatha, as far I could gather it should be a Vinaya commentary. Does someone have a full English translation of it? I would be interested in how it deals with kalapas.
This (Parajikan Atthakatha) is available within Samantapāsādikā more particularly the part called Parajikakanda Atthakatha. The original is published by PTS and available in Pali at the Pariyatti Store. As for an English translation there is: The Inception of Discipline &amp; the Vinaya Nidana: Being a Translation &amp; Edition of the Bahiranidana of Buddhaghosa's Samantapasadika, the Vinaya Commentary (Sacred Books of the Buddhists). (Link to Inception of Discipline N.A. Jayawickrama at Pariyatti Store) I am not sure if this is complete and thorough thought as the original is a 8 volume set which seems to be condensed to 1 volume in the English translation. If you are looking fro free editions both (Pali and english) are available in https://archive.org/ which I have given the links above.

Probably U Ba Khin is referring to the following passage (PDF from Parajikakanda Atthakatha, page 160):


  Evaṃ nāmarūpaṃ vavatthapetvā tassa paccayaṃ pariyesati, pariyesanto ca taṃ disvā tīsupi addhāsu
  nāmarūpassa pavattiṃ ārabbha kaṅkhaṃ vitarati. Vitiṇṇakaṅkho kalāpasammasanavasena tilakkhaṇaṃ āropetvā
  udayabbayānupassanāya pubbabhāge uppanne obhāsādayo dasa vipassanupakkilese pahāya upakkilesavimuttaṃ
  paṭipadāñāṇaṃ ‘‘maggo’’ti vavatthapetvā udayaṃ pahāya bhaṅgānupassanaṃ patvā nirantaraṃ bhaṅgānupassanena
  bhayato upaṭṭhitesu sabbasaṅkhāresu nibbindanto virajjanto vimuccanto yathākkamaṃ cattāro ariyamagge
  pāpuṇitvā arahattaphale patiṭṭhāya ekūnavīsatibhedassa paccavekkhaṇañāṇassa pariyantappatto sadevakassa lokassa
  aggadakkhiṇeyyo hoti. Ettāvatā cassa gaṇanaṃ ādiṃ katvā vipassanāpariyosānā ānāpānassatisamādhibhāvanā ca samattā hotīti.


That turns out to be a quote from Visuddhimagga (viii-224 and viii-225), part of a commentary on the first tetrad of anapana meditation. The English Bhikkhu Ñánamoli’s translation is the following:


  
  Having defined mentality-materiality in this way, he seeks its condition. With search he finds it, and so overcomes his doubts about
  the way of mentalitymateriality’s occurrence in the three divisions of
  time (Ch. XIX). His doubts being overcome, he attributes the three
  characteristics [beginning with that of suffering to mentality and
  materiality], comprehending [them] by groups (XX.2f.); he abandons the
  ten imperfections of insight beginning with illumination, which arise
  in the first stages of the contemplation of rise and fall (XX.105f.),
  and he defines as “the path” the knowledge of the way that is free
  from these imperfections (XX.126f.). He reaches contemplation of
  dissolution by abandoning [attention to] arising. When all formations
  have appeared as terror owing to the contemplation of their incessant
  dissolution, he becomes dispassionate towards them (Ch. XXI), his
  greed for them fades away, and he is liberated from them (Ch. XXII).
  After he has [thus] reached the four noble paths in due succession and
  has become established in the fruition of Arahantship, he at last
  attains to the nineteen kinds of reviewing knowledge (XXII.19f.), and
  he becomes fit to receive the highest gifts from the world with its
  deities.
  At this point his development of concentration through mindfulness of breathing, beginning with counting and ending with
  looking back (§189) is completed.