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The archive contains little scientific material as by far the greater part of Thomson's scientific papers are deposited in Cambridge University Library. Material is arranged as follows:
Section A - Personal material and correspondence;
Section B - Notes and drafts for publication;
Section C - Scientific correspondence;
Section D - Accounts and biographies of Thomson;
Section E - Published works.

The material in this collection covers the period 1836-1958. It is presented in eight sections.

Section A, Biographical, covers the period 1874-1958. The material includes biographical profiles, certificates, press cuttings, photographs and invitations. Correspondence and papers used by Lord Rayleigh in the preparation of his biography of Thomson The Life of Sir J. J. Thomson O.M. sometime master of Trinity College, Cambridge (Cambridge, 1942) can be found at A/23-A31. A/110-A/143 include press cuttings on Thomson's lectures and reviews of his publications. Certificates are at A/72-A/103

Section B, Family and personal, is the largest in the collection and spans the period 1836-1952. The bulk of the material consists of family and personal correspondence sent to members of the Thomson and Paget families between 1872 and 1952. This correspondence has been arranged by recipient, thus for example, letters from Thomson to his wife are to be found in Lady Thomson's correspondence at B/45-B/53 rather than in that of Thomson himself (B/1-B/6). There is significant correspondence sent to Thomson, 1873-1940, but the largest component of the section, at B/45-B/639, is correspondence and papers of Lady Thomson covering the period 1872-1950. This includes family and personal correspondence received by Lady Thomson, notebooks and diaries, and correspondence from societies and organisations. At B/640-B/679 is correspondence received by other family members including G.P. Thomson, J.P. Thomson, F.V. Thomson and G.E. Paget. The section also includes photographs, household accounts and a little miscellaneous material.

Section C, Trinity College, Cambridge, consists chiefly of incoming correspondence sent to Thomson as Master of Trinity College, Cambridge and covers the period 1918-1944. The bulk relates to College matters including students, Fellows, meetings etc., but there is also business and personal correspondence including letters of congratulations on Thomson's installation as Master in 1918. The correspondence includes letters from Cambridge colleagues such as E. Rutherford, R.T. Glazebrook, J.G. Frazer and A. Schuster. The section also includes invitations to social occasions received by the Thomsons and replies to invitations to social events hosted by the Thomsons between 1918 and 1938. There are also a small number of Trinity College entrance examination papers and scripts.

Section D, Research, is very slight. It consists of a few research notes and photographs for the period 1893 to 1934.

Section E, Societies and organisations, is also slight. It has been arranged in alphabetical order and covers the period 1886-1930. The most significant material is that at E/10-E/28: reports and minutes of the Committee on Science in the Educational System of Great Britain, which Thomson chaired between 1902 and 1920. There is also a small amount of Royal Society material.

Section F, Lectures, speeches and publications, covers the period 1876-1938. There is material on a number of Thomson's public lectures and speeches including lectures given at the British Association for the Advancement of Science annual meeting in Winnipeg, Canada, 1909. A notebook at F/27 has typescript notes on lectures delivered at Cambridge by Thomson. Publications material includes manuscript drafts of the first edition of Conduction of Electricity through Gases (Cambridge 1903) and Rays of Positive Electricity (London 1913). Press cuttings on Thomson's lectures and publications can be found at A/110-A/143.

Section G, Visits and conferences, is not extensive. The material has been arranged in chronological order 1896-1938. It includes brief correspondence on the British Association for the Advancement of Science annual meeting, 1909.

Section H, Correspondence, is presented in two sequences, scientific and general. The scientific sequence includes letters from G. G. Stokes, Lord Rayleigh (4th Baron) and Lord Kelvin. The general sequence is arranged in chronological order covering the period 1888-1938. A file of 'Letters to JJ from distinguished people and others' is at H/32-H/35, which includes correspondence from Arthur Balfour, Stanley Baldwin and Austen Chamberlain.

Section A, Biographical, includes letters from the King George VI’s Private Secretary informing Thomson of the King’s wish to award him the Order of Merit. There are also press cuttings relating to Thomson and material concerning dinners and functions at Cambridge University.

Section B, Family and personal, chiefly consists of correspondence sent to Thomson’s wife, Rose, and to his brother Frederick. The former group of correspondence dates from 1882 to 1949 and comprises letters to Lady Thomson from various members of her family, including her twin sister, Violet, and letters of thanks for hospitality at Trinity College from visiting academics, scientists, politicians and others. The letters to Frederick Thomson are from Lady Thomson and date from 1906 to 1914. There are a few letters, 1903, from Thomson to his wife.

Section C, Correspondence, is presented in two sequences: general correspondence to Thomson dating from 1886 to 1939 and correspondence in French with foreign scientists 1898-1926. The general correspondence is from various scientists, politicians and academics, a large part of it being letters of thanks for hospitality at Trinity College. The correspondence in French, of both Thomson and his wife, is with a number of distinguished scientists, or their spouses, including Marie Curie, A.H. Becquerel and Paul Langevin.

Section D, Non-text material, has one item only: a film of Thomson delivering a lecture in 1934. There is also an index of correspondents.