DANIELE MACUGLIA
Contact me

DANIELE MACUGLIA

Contact me
immagine copertina mobile Publications

Publications & Talks


Research articles

11 — “The Birth of SHAKE and the Exact Solution of the Dynamics of Semi-Rigid (Bio)Molecules in Cartesian Coordinates,” (in preparation).

This article traces the history of early molecular dynamics (MD) simulations in biology, specifically exploring the development of SHAKE, a constraint-based technique developed in 1976 by Jean-Paul Ryckaert, Giovanni Ciccotti and the late Herman Berendsen at CECAM (Centre Européen de Calcul Atomique et Moléculaire). With currently over 20,000 citations, the work of the three scientists proved to be instrumental in giving impetus to the MD simulation of complex polymer systems and currently underpins the work of thousands of researchers worldwide engaged in computational physics, chemistry and biology. Despite its impact and its role in bringing different scientific fields together—thus representing a privileged vantage point from which to study the development of biology in the 20th century—accurate historical studies on the birth of SHAKE are virtually absent. By collecting and elaborating on the accounts of Ryckaert and Ciccotti, this essay aims to fill this gap, while also commenting on the conceptual and computational difficulties faced by its developers.

10 — “The Emergence of Protein Dynamics Simulations: How Computational Statistical Mechanics Met Biochemistry,” with Benoît Roux and Giovanni Ciccotti. Accepted in the European Physical Journal H, 2022 (forthcoming).

In this essay we aim to illustrate how Martin Karplus and his research group have effectively set in motion the engine of molecular dynamics (MD) simulations of biomolecules. This process saw its prodromes between 1969 and the early 1970s with Karplus’ landing in biology, a transition that came to fruition with the treatment of 11-cis-retinal photoisomerization and the development of an allosteric model to account for the mechanism of cooperativity in hemoglobin. In 1977, J. Andrew McCammon, Bruce Gelin, and Martin Karplus published an article in Nature reporting the MD simulation of bovine pancreatic trypsin inhibitor (BPTI). This publication helped initiate the merger of computational statistical mechanics and biochemistry, a process that Karplus undertook at a later stage and whose beginnings we propose to reconstruct in this essay through unpublished accounts of the key people who participated in this endeavor.

09 — “The Universe: A Book Written in the Mathematical –and the Programming– Language,” Il Nuovo Cimento C, 2021, Vol. 44, No. 1, article number 25.

This paper concerns the pronounced shift that occurred, in the twentieth century, from the formulation of scientific laws with limited computational capabilities —a distinctive trend of the early and late modern periods— to the formulation and the massive computation that we can now perform with the aid of computer technologies. This change altered our relationship with science, and thus our ambitions with nature. What seems clear is that the universe —the “grand book” that “stands continually open to our gaze”— is not solely written with “triangles, circles, and other geometric figures”, as Galileo Galilei put it, but also with languages whose characters consist of data, processes, structures and other constructs of computer programs without which we would now wander about “in a dark labyrinth”.

08 — “The Breakthrough of a Quantum Chemist by Classical Dynamics: Martin Karplus and the Birth of Computer Simulations of Chemical Reactions,” with Benoît Roux and Giovanni Ciccotti. European Physical Journal H, 2021, Vol. 46, article number 12.

1964–1965 was an early, crucial period in Martin Karplus’ research—a time when, rather unexpectedly, he approached the problem of reactive collisions using a quasiclassical approximation with the aid of computer technologies. This marked a substantial departure from the quantum-chemical studies of nuclear magnetic resonance that had, until then, dominated his work. The historical perspective outlined by George Schatz, as well Karplus’ own biography, partly frames the contours of this remarkable period in the history of theoretical chemistry. Yet, the available historical literature is not sufficiently complete to allow us to understand Karplus’ transition from nuclear magnetic resonance to reaction dynamics. In this article, we discuss the intellectual ground on which Karplus operated around 1964, further commenting on the relevance of his quantum and quasiclassical studies and pondering how Karplus’ approach eventually led to his interest in the simulation of complex biomolecules.

07 — “Sense Experiences and ‘Necessary Simulations:’ Four Centuries of Scientific Change from Galileo to Fundamental Computer Simulations,” with Benoît Roux and Giovanni Ciccotti, KNOW: A Journal on the Formation of Knowledge, 2020, Vol 4, No. 1, pp. 63–87.

This article evaluates the impact of fundamental computer simulations on theoretical physics, pondering whether fundamental computer simulations can be considered sufficiently consequential to have caused a revolutionary occurrence in the twentieth-century history of science.

06 — “Newtonianism and Information Control in Rome at the Wake of the Eighteenth Century,” Annals of Science, 2020, Vol. 77, No. 1, pp. 108–126.

This paper offers an opportunity for reconstructing and commenting on relevant details around the way in which the Italian institutional background—particularly the presence of the Church and its methods of information control—shaped the dissemination and practice of Newtonian science in early modern Italy, with particular attention to the first half of the eighteenth century.

05 — “Talking about Secrets: The Hanford Nuclear Facility and News Reporting of Silence, 1945-1989,” in Felicity Mellor and Stephen Webster, eds., The Silences of Science: Gaps and Pauses in the Communication of Science (New York: Routledge, 2017), pp. 115–134.

In this book chapter I demonstrate the ways in which the Hanford Nuclear Works existed in a communicative context of “partial silence,” a middle ground between “knowing” and “not knowing,” from the end of the Second World War to the end of the Cold War. In particular, in this essay I investigate how the qualities and meanings of such a silence altered over time, impacting public understanding of nuclear research and environmental hazards.

04 — “The Work of the Roman Newtonians in the Italian Enlightenment,” Viewpoint: Magazine of the British Society for the History of Science, 2015, Vol. 108, pp. 8–9.

This short piece offers an introductory overview of the early modern intellectual milieu in Rome at the time of Francesco Bianchini and Celestino Galiani. In this essay, I stress the reasons why this backdrop proved fundamental to the spread of Newtonianism in early modern Italy.

03 — “Corrado Gini and the Scientific Basis of Fascist Racism,” Medicina nei Secoli Arte e Scienza, 2014, Vol. 26, No. 3, pp. 821–856.

I wrote this essay as a graduate student attending seminars in the history of medicine at the University of Chicago. In this study, I focus on the controversial figure of Corrado Gini, who had a tremendous influence on Benito Mussolini’s political campaign, shaping Italian social sciences for almost two decades. The paper offers a reconstruction of some significant aspects around the scientific debates surrounding the establishment of fascism and racism.

02 — “Hanford and the middle ground between ‘knowing’ and ‘not knowing,’Bulletin of the Atomic Scientists, “Voices of Tomorrow,” Oct. 31, 2013.

In this essay, I focus on the communities living around the Hanford Site, showing that local people had an understanding of the environmental hazards posed by the nuclear facility before the end of the Cold War. However, they could not really on all the tools necessary to develop a clear and uncontroversial understanding of this hazardous situation. In my study, I show how specific “drivers of secrecy” have shaped the history of the Hanford nuclear facility, immediately after the Second World War.

01 — (In German) “Die nukleare Anlagen von Hanford (1943–1987): Eine Fallstudie über die Schnittstellen von Physik, Biologie und die US-amerikanische Gesellschaft zur Zeit des Kalten Krieges,” in Christian Forstner and Dieter Hoffmann, eds., Physik im Kalten Krieg (Berlin: Springer Spektrum, 2013), pp. 77–87.

In this book chapter, I focus on the social dimension of the nuclear hazards posed by the Hanford Site, analyzing newspaper archives (particularly The Seattle Times and The New York Times) and discussing public understanding of nuclear research. I also focus on social movements around nuclear research, useful to frame the rise of twentieth century environmental concerns in US history.

Smaller pieces

12 — Giovanni Battimelli, Giovanni Ciccotti, and Pietro Greco’s Computer Meets Theoretical Physics: New Frontier of Molecular Simulation, Isis: A Journal of the History of Science Society, 2022, Vol. 113, No. 2, pp. 461–462.

11 — Hannah Marcus’ Forbidden Knowledge: Medicine, Science, and Censorship in Early Modern Italy, Isis: A Journal of the History of Science Society, 2022, Vol. 113, No. 2, pp. 436–437.

10 — “Zucchi, Niccolò,” Dizionario Biografico degli Italiani. Enciclopedia Treccani (2021).

09 — “Zamboni, Giuseppe,” Dizionario Biografico degli Italiani. Enciclopedia Treccani (2021).

08 — “Margulis, Lynn,” in Hugh R. Slotten, ed., Oxford Encyclopedia of the History of American Science, Medicine, and Technology (New York and Oxford: Oxford University Press, 2014), Vol. 2, pp. 21–22.

07 — “Menard, Henry William,” in Hugh R. Slotten, ed., Oxford Encyclopedia of the History of American Science, Medicine, and Technology (New York and Oxford: Oxford University Press, 2014), vol. 2, pp. 78–79.

06 — Dom Paschal Scotti’s Galileo Revisited: The Galileo Affair in Context, Reading Religion, March 31, 2018, online. 

05 — David Norbrook, Stephen Harrison, and Philip Hardie’s Lucretius and the Early Modern, Renaissance Quarterly, 2017, Vol. 70, No. 1, pp. 249–251.

04 — Owen Gingerich’s Gods Planet, The Quarterly Review of Biology, 2015, Vol. 90, No. 3, pp. 315–316.

03 — Keith Parsons’ It Started with Copernicus: Vital Questions about Science, The Quarterly Review of Biology, 2015, Vol. 90, No. 2, p. 201.

02 — Crystal Hall’s Galileos Reading, Annali dItalianistica, 2015, Vol. 33, pp. 459–461.

01 — Richard Dawkins’ The Magic of Reality: How We Know Whats Really True, The Quarterly Review of Biology, 2012, Vol. 87, No. 4, p. 402.