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Manuel N. Melo Lab

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The Multiscale Modeling Lab employs computational molecular simulation models at different resolution scales to tackle a wide range of biological questions.

Manuel N. Melo
Investigador Auxiliar
PhD in 2010,Universidade de Lisboa

Phone (+351) 214469616 | Extension 1616



Research Interests

The Multiscale Modeling Lab employs computational molecular simulation models at different resolution scales to tackle a wide range of biological questions. The main research focus is the behavior of biological membranes, of proteins, and of membrane-embedded proteins. Applications range from the prediction of biophysical properties of membranes of different composition, to the study of protein association and aggregation, to the functional characterization of large protein-membrane assemblies such as those involved in photosynthesis.

The time and length scales that govern these systems can be of the order of tens of nanometers, and hundreds of microseconds. To be tractable, molecular-level simulations of such magnitude require the use of simplified models: we employ and co-develop the Martini coarse-grain model, in which individual chemical groups are simplified as being single "super" atoms. This reduction in system complexity can yield a performance speed-up close to 1000x, as compared to models with full atomistic detail.

The use of a coarse-grain model can sometimes limit the physiological relevance of a simulated system. When finer detail is needed, it is possible to 1) convert a coarse-grain system into a full-detail representation or 2) simulate  a system partly at coarse-grain detail, partly at fine-grain detail. At our lab effort is actively being put into perfecting this last multi-resolution approach.


Group Members

Clément Arnarez, Post-Doc

Marcin Makowski, PhD Student (collaboration with IMM)

Nestor Wendt, Research Fellow


Selected Publications

  1. The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission
    J Su, AS Thomas, T Grabietz, C Landgraf, R Volkmer, SJ Marrink, C Williams, MN Melo
    Biochimica et Biophysica Acta (BBA) - Biomembranes 1860 (6), 1292-1300

  2. Lipid organization of the plasma membrane
    HI Ingólfsson, MN Melo, et al.
    Journal of the american chemical society 136 (41), 14554-14559
  3. Parameters for Martini sterols and hopanoids based on a virtual-site description
    MN Melo, HI Ingólfsson, SJ Marrink
    The Journal of chemical physics 143 (24), 243152


Laboratory's Website

For further information please visit the laboratory's website


Modelação Multiescala (PT)

O Laboratório de Modelação Multiescala usa modelos computacionais com vários níveis de detalhe, para dar resposta a uma larga gama de perguntas biológicas. Focamo-nos no estudo de membranas biológicas, de proteínas, e de proteínas membranares, e pretendemos dar resposta a perguntas como De que modo dependem as propriedades de uma membrana da sua constituição? Como interatuam determinadas proteínas umas com as outras e como podemos controlar esse processo? Quais as características que permitem o funcionamento eficiente de grandes complexos proteína-membrana, como os responsáveis pela fotossíntese?

Em concreto, são usados modelos coarse-grain -- nos quais cada grupo químico é considerado, simplificadamente, como uma única partícula -- para se conseguir simular os grandes tamanhos e durações dos processos em estudo. Quando um sistema requer detalhe atomístico há possibilidade de 1) transformá-lo de uma representação coarse-grain para uma representação com todo detalhe, ou 2) simular uma região do sistema com detalhe atomístico e o resto com detalhe coarse-grain. O nosso laboratório dedica-se, em particular, a aperfeiçoar este tipo de metodologias para simulação multi-resolução.


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