Medical Systems Biophysics and Bioengineering

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Welcome to the Mashaghi lab!


Our group is conducting research at the interface of physics, engineering and medicine. We develop and use theoretical, computational, and experimental approaches to address fundamental and applied research problems relevant to human pathologies. Fundamental research in our lab is focused on the single-molecule and topology analysis of biomolecular structure and dynamics. In particular, how fold topology defines the biology and physics of proteins, genome, and biomolecular condensates, and how molecular fold topology is regulated in cellular environment (e.g., by molecular chaperones). Other areas of interest are single-cell analysis of mechanics and metabolism, mechano-immunology, and mechano-pharmacology. We are also interested in systems biophysics and complex biological networks.

Applied research in our group is focused on medical diagnostics, chip-based disease models, and nano-medicine. Specifically, we are developing innovative engineering approaches to fight emerging viral diseases.


The Mashaghi lab is a part of Leiden Academic Centre for Drug Research, one of the world's leading institutes in the field of pharmaceutical sciences. We are also a founding partner of the Centre for Interdisciplinary Genome Research.

Selected Publications

Evers T, Sheikhhassani V, Haks MC, Storm C, Ottenhoff THM, Mashaghi A, Single cell analysis reveals chemokine mediated differential regulation of monocyte mechanics. iScience 25(1) 103555 (2022)

Heidari M, Moes D, Schullian O, Scalvini B, Mashaghi A, A topology framework for macromolecular complexes and condensates.

Nano Research (2022)

Evers T, Holt L, Alberti S, Mashaghi A, Reciprocal regulation of cellular mechanics and metabolism. Nature Metabolism 3, 456–468 (2021)

Heidari M, Schiessel H, Mashaghi A, Circuit topology analysis of polymer folding reactions. ACS Central Science 2(7) P609-622 (2020)

Junaid A, Tang H, van Reeuwijk A, Abouleila Y, Wuelfroth P, van Duinen V, Stam W, van Zonneveld AJ, Hankemeier T, Mashaghi A, Ebola Hemorrhagic Shock Syndrome-on-a-Chip. iScience 23(1), 100765 (2020)

Heidari M, Satarifard V, Mashaghi A, Mapping a single-molecule folding process onto a topological space. Physical Chemistry Chemical Physics 21 (36), 20338-20345 (2019)

Mashaghi A and Ramezanpour A, Statistical physics of medical diagnostics: Study of a probabilistic model. Physical Review E 97 (3), 032118 (2018)

Ghafari M and Mashaghi A, On the role of topology in regulating transcriptional cascades. Physical Chemistry Chemical Physics 19, 25168-25179 (2017)

Mashaghi A, Bezrukavnikov S, Minde DP, Wentink AS et al., Alternative modes of client binding enable functional plasticity of Hsp70, Nature 539, 448–451 (2016)

Nikoofard N, Mashaghi A, Topology sorting and characterization of folded polymers using nano-pores, Nanoscale 8, 4643-4649 (2016)