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S1: He became a physicist in 2000, since when he had done research on the molecular theories. However, he decided to abandon his physics career for personal reasons.

S2: He had done research on the molecular theories since he became a physicist in 2000. However, he decided to abandon his physics career for personal reasons.

Q1: Do S1&S2 mean almost identically with little difference in meaning except grammar structure?

Q2: Is it possible for “Past perfect” to be used carrying the meaning---time period of an action/event with its starting point in the past & ending point still in the past?

or Do I have to use “had been doing,” i.e. past perfect progressive to emphasize the duration/span of doing research?

ref: https://www.ldoceonline.com/dictionary/by-since-when

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In your first example

S1:He became a physicist in 2000, since when he had done research on the molecular theories. However, he decided to abandon his physics career for personal reasons.

it would be better to write had been doing research if you believe it to have occupied all or most of the time until he abandoned. In fact I would almost say had done was incorrect here.

In your second example

S2:He had done research on the molecular theories since he became a physicist in 2000. However, he decided to abandon his physics career for personal reasons.

Using had done seems more natural but had been doing would be fine and the equivalent.

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  • Thank you, Mdewey. I agree with you on the explanation of S1. Would you please elaborate more about why "had been doing" instead of "had done" is grammatically acceptable, as in S1, while both tense makes little difference in meaning as shown in S2?
    – Yunhui Lan
    Aug 9, 2020 at 14:41
  • It seemed to me that by altering the order of the concepts you also altered the emphasis and hence the timing of the activities.
    – mdewey
    Aug 9, 2020 at 15:51
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Simple Past and Past Perfect show past actions, but in different ways. Simple Past shows a specific past action usually with a time reference, whereas, Past Perfect shows an action in the long past.

He had done research in molecular theories before he became a physicist in 2000. It means, even before he became a physicist, he had done research.

I had taught in small educational institutes even before I got a teacher's position. This means, even before I became a teacher, I had taught.

This is the usual way of using Past Perfect and Simple Past. I think your confusion is about this. I haven't touched your examples since they are a little confusing to me.

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  • Thank u, Ram. I know the difference of usage in past simple & past perfect. Both talk about the past action or event. However, past perfect precedes past simple. What i want want to know is, can I use past perfect progressive “had been doing research”instead of “had done research”to match the above-mentioned context?
    – Yunhui Lan
    Aug 9, 2020 at 12:14
  • Past perfect progressive (Past perfect continuous), is the past counter-part of "present perfect continuous". A typical example here is, "I had been working for Xerox India in the nineties." It shows an action 'that was progressing for a duration in the (long) past'. You can use it here too, like " He had been doing research in .... before he became a physicist in 2000.
    – Ram Pillai
    Aug 9, 2020 at 15:29

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