Scientific Computing & Big Data

We exploit parallel computing on single and multi Graphic Processing Units (GPU’s) for several problems. In particular, we develop optimised parallel codes for continuous variables Monte Carlo dynamics, Population dynamics for Belief propagation and Cavity method in random graphs, and Pseudolikelihood maximisation.

 

Algorithms. We are interested in the development of efficient computational techniques for the study of inference and optimization problems in large experimental data bases, mostly for complex biological systems. Among the key application domains are the analysis of gene expression at single cell resolution, the study of kinetic and/or thermodynamical conservation laws in cellular metabolic networks, the analysis of evolutionary variability in protein sequences, the characterization of cell-to-cell variability in microbial populations (at both the physiological and the molecular level), and the inference of complex interaction networks (protein-protein, protein-DNA, RNA-RNA) from genomic and/or thermodynamic data. In addition, we work on the development of multi-scale models for metabolic engineering of unicellular organisms and large-scale simulation of human tissues.

 

Biophysical simulations: Molecular competition on receptors. Many biological processes are based on the interaction between a receptor and various partner molecules that can bind it. To clarify these interactions, ‘in vitro’ experiments usually analyze the receptor in the presence of another single molecule. Nevertheless, ‘in vivo’ mechanisms are much more complex, and there can be competition phenomena among different molecular partners for the same receptor, or among different molecules of the same type that could associate to distinct regions of the same receptors through various binding modes. Computer simulations can help in a systematical mapping of the various possible combinations.

Facilities and Labs

S.Li.M. Lab @ Roma

People

Andrea_DeMArtinoAndrea

De Martino

CNR Researcher

Bruno_RizzutiBruno

Rizzuti

CNR Researcher

leuzziLuca

Leuzzi

CNR Researcher

fabrizioantenucci_postdocFabrizio

Antenucci

Associate PostDoc

alessiamarruzzo_postdocAlessia

Marruzzo

Associate PostDoc

Publications

  1. S. Evoli, D.L. Mobley, R. Guzzi, B. Rizzuti, Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations, bioRxiv, 8, 1-27, (2016) doi:10.1101/068502.
  2. Regularization and decimation pseudolikelihood approaches to statistical inference in XY-spin models, P Tyagi, A Marruzzo, A Pagnani, F Antenucci, L Leuzzi, Physical Review B 94, 024203 (2016), Doi: 10.1103/PhysRevB.94.024203.
  3.  Multi-body quenched disordered XY and p-clock models on random graphs. A Marruzzo, L Leuzzi, Physical Review B 93, 094206 (2016) Doi: 10.1103/PhysRevB.93.094206.
  4.  M Mori, T Hwa, OC Martin, A De Martino and E Marinari. Constrained Allocation Flux Balance Anal- ysis. PLoS Comp Biol 12:e1004913 (2016) Doi: 10.1371/journal.pcbi.1004913
  5. A Martirosyan, M Figliuzzi, E Marinari and A De Martino. Probing the limits to microRNA-mediated control of gene expression. PLoS Comp Biol 12: e1004715 (2016) Doi: 10.1371/journal.pcbi.1004715
  6. Nonlinear XY and p-clock models on sparse random graphs: Mode-locking transition of localized waves, A Marruzzo, L Leuzzi, Physical Review B 91, 054201 (2015) Doi: 10.1103/PhysRevB.91.054201
  7. Statistical mechanical theory of mode-locked multimode lasers in closed cavity: determination of thresholds, spectra, pulse phase delays and pulse correlations. F Antenucci, M Ibanez Berganza, L Leuzzi, Phys. Rev. A 91, 043811 (2014) Doi:.10.1103/PhysRevA.91.043811
  8. D De Martino, F Capuani and A De Martino. Inferring metabolic phenotypes from the exometabolome through a thermodynamic variational principle. New J Phys 16: 115018 (2014) Doi: 10.1088/1367-2630/16/11/115018
  9. A De Martino, D De Martino, R Mulet and A Pagnani. Identifying all moiety conservation laws in genome-scale metabolic networks, PLoS ONE 9:e100750  (2014)  Doi: 10.1371/journal.pone.0100750
  10. A Seganti, F Ricci Tersenghi and A De Martino. Searching for feasible stationary states in reaction net- works by solving a Boolean constraint satisfaction problem. Phys Rev E 89:022139 (2014) Doi: 10.1103/PhysRevE.89.022139

Other selected publications

  1. FA Massucci, M DiNuzzo, F Giove, B Maraviglia, I Perez Castillo, E Marinari and A De Martino. Energy metabolism and glutamate-glutamine cycle in the brain: a stoichiometric modeling perspective. BMC Sys Biol 7:103 (2013) Doi: 10.1186/1752-0509-7-103
  2. D De Martino, F Capuani, M Mori, A De Martino and E Marinari. Counting and correcting thermody- namically infeasible flux cycles in genome-scale metabolic networks. Metabolites 3:946 (2013) Doi: 10.3390/metabo3040946
  3. FA Massucci, F Font Clos, A De Martino and I Perez Castillo. A novel methodology to estimate metabolic flux distributions in constraint-based models. Metabolites 3:838 (2013) Doi: 10.3390/metabo3030838
  4. A Seganti, A De Martino and F Ricci Tersenghi. Boolean constraint satisfaction problems for reaction networks. J Stat Mech P09009 (2013) Doi:10.1088/1742-5468/2013/09/P09009
  5. D De Martino, M Figliuzzi, A De Martino and E Marinari. A scalable algorithm to explore the Gibbs energy landscape of genome-scale metabolic networks. PLoS Comp Biol 8:e1002562 (2012) Doi: 10.1371/journal.pcbi.1002562

Latest News

Loretta del Mercato, si aggiudica l'ERC STARTING GRANT 2017

Loretta del Mercato, si aggiudica  l'ERC STARTING GRANT 2017

uno dei bandi più competitivi a livello europeo.

Lecce, 6 settembre 2017 

Lo European Research Council, che promuove la ricerca di eccellenza in Europa, nei giorni scorsi ha reso noti i nomi dei 406 vincitori della selezione ERC STARTING GRANT 2017, il bando tra i più competitivi a livello internazionale.

Su 3085 progetti presentati, 406 i progetti selezionati a cui sono stati destinati i 605 i milioni di euro di investimento. 48 le nazioni di provenienza dei ricercatori, soltanto 17 gli Italiani che condurranno le loro ricerche nel nostro paese, tra cui Loretta del Mercato, ricercatrice dell'Istituto di Nanotecnologia del Consiglio Nazionale delle Ricerche di Lecce.

Un importante riconoscimento alla ricerca nel settore della medicina di precisione condotta presso il CNR NANOTEC, un indiscusso premio al talento della giovane ricercatrice che, a 38 anni e un contratto a tempo determinato, sarà a capo del progetto "Sensing cell-cell interaction heterogeneity in 3D tumor models: towards precision medicine – INTERCELLMED".

Il progetto, il cui obiettivo è affrontare uno dei problemi più spinosi della ricerca sul cancro, ovvero la difficoltà nel trasformare i risultati delle ricerche scientifiche in applicazioni cliniche per i pazienti e che vedrà coinvolto l'Istituto tumori "Giovanni Paolo II" di Bari, si propone di sviluppare nuovi modelli in vitro 3D di tumore del pancreas, alternativi ai modelli animali, ingegnerizzati con un set di sensori nanotecnologici che consentiranno di monitorare le interazioni delle cellule tumorali con il loro micorambiente, verificare l'appropriatezza delle terapie prima della somministrazione ai pazienti oncologici e quindi prevedere la risposta dei singoli pazienti ad una o più terapie antitumorali.

La realizzazione di queste piattaforme 3D multifunzionali consentirà di superare le evidenti differenze intercorrenti tra "modelli animali" ed esseri umani fornendo dati attendibili ed in tempi più rapidi rispetto ai dati ottenuti tramite lunghi e costosi procedimenti di sperimentazione sugli animali. Le tecnologie e i modelli sviluppati saranno estesi anche ad altre forme di tumori solidi nonché impiegati per studi nell'ambito della ingegneria tissutale e della medicina rigenerativa.

Rassegna stampa e Video

Zeiss Microscopy Technology and Complete Correlative Workflow

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Zeiss Microscopy Technology and Complete Correlative Workflow

Lecce, Italy, 2017 Wednesday July 19th 

CNR NANOTEC @ Lecce, Aula Seminari – pal. G, Piano Terra

Program - PDF

Zeiss, as microscopy technology leader, provides the unique complete imaging solution ranging from light, confocal, electron, ion and Xray modalities with a complete and straightforward correlative workflow. An overview of different technologies will be presented with a special focus on X-Rray microscopy.

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MCS 2017

International Workshop on Micropropulsion and CubeSats

Bari, Italy, 26 - 27 June 2017

Program - MSC2017

This narrow-field, invited-only meeting is the first attempt to bring together the Materials and Micropropulsion communities with a view to contribute to the development of the Global Materials and Micropropulsion Roadmap, and set such meetings to a regular basis.