modeling nature from nano to macro
Infrastructures & Facilities
Regarding the facilities from both the research and training perspectives, MNat has excellent laboratories and university departments. MNat has internationally recognized training programs (master and doctorate), which are an international reference because of their quality. As an example, more than 65% of students are attracted from outside the scope of UGR and more than 35% come from universities in other countries.
The resources and services might include libraries, reading and meeting rooms, computer rooms and other similar facilities necessary to carry out activities of exhibition and defence of work plans, seminars and conferences, the latter equipped with the most advanced audiovisual media. The infrastructures and material resources available also include laboratories and scientific equipment necessary for the execution of the work plans proposed by the students within the different lines of research that are developed in our Programs.
MNat’s master and doctoral programs have been evaluated by the Spanish Government, obtaining the best qualifications and leading their respective areas.
MNat’s laboratories, like all other resources, are connected with each other and complementary around the four pivotal lines which form the basis of MNat. As an example, in the research and treatment of marine aggregates, in addition to the resources of the Ecology laboratories MNat is using elasticity and plasticity studies from the Fluids and Biocoloids laboratory, as well as resistance and porosity analysis from the Nanoelectronics laboratory. This process is also being carried out in the field of the mechanical properties of tumor cells as opposed to non-tumor cells, where, in addition to the Biomedical laboratory and those mentioned above, the Ultrasonics laboratory is involved in the analysis of wave-tumor interactions. The potential of MNat laboratories is growing significantly in the period 2015-2019 in which the Unit has received more than EUR 4.5 million investment in infrastructure to expand its capabilities. In addition to MNat own laboratories, the Unit has the facilities granted by the Center for Scientific Instrumentation at UGR, which provides very useful and modern means to carry out the tasks. One of the consequences of the eventual MNat awarding with the mention 'María de Maeztu' would be the acceleration of the project to unify its different laboratories in the same area. On the other hand, MNat’s laboratories are connected to those most internationally advanced on each of the research topics, either through agreements or collaborations.
Some of the features of MNat laboratories are:
1) The Biomedical laboratory is located in the Biomedical Research Centre (CIBM) of the Granada Health Technology Park (PTS), and enables activation of target genes, clustering in cell signaling, cell mechanics, mechanical waves and cell interaction, tumor stem cells, regeneration, and microenvironment on living cultures with laminar flow cabinets and stoves. CIBM has an extensive range of state-of-the-art techniques (centrally located, properly maintained and managed by experts). These include cutting edge laboratories for cellular and molecular studies equipped with: laminar flow hoods; cell incubators; cold chambers; fridges and freezers (+4º/-20°/-80ºC); refrigerated micro- and ultra-centrifuges; sonicators; magnetic stirrers; precision balances; pH meters; cryostats; UV transilluminators; vertical electrophoresis systems; liquid nitrogen containers; spectrophotometers; confocal and fluorescence microscopes; plate readers; qPCR systems; Luminex 200 Systems, etc. Also, the CIBM includes GLP3 suite; a Flow Cytometry unit (equipped with FACSCalibur and FACSCanto Cell sorters and analyzers); animal experimentation facility with a surface of 800m2; IVIS facility; sample processing and pathology services for histological studies. Seminar rooms and theatres are also available to the fellow. CIBM houses the Node Coordination of Biobank of the Andalusia Public Health System that offers fresh, frozen and fixed samples derived from patients with neoplastic diseases. Moreover, since the hosting group is member of the Institute of Bio-sanitary Research (ibs.GRANADA, http://www.ibsgranada.es/), it has access to three scientific platforms: clinical trials and clinical epidemiology; biobanking and disease register; and scientific and technical services. Finally, the group has full access to other analysis and imaging techniques at the Center for Scientific Instrumentation (http://cic.ugr.es) at UGR.
2) The Nanoelectronics, Graphene and 2D materials at the UGR is a dynamic and international group ideally located within an outstanding multidisciplinary research environment with strong collaborations with the Chemistry, Physics, Electronics and Medicine departments, the Center for Scientific Instrumentation at the UGR, and the Institute for BioHealth Research of Granada. The Nanoelectronics group is composed of 14 staff members with long record in the hosting and integrating of postdoctoral researchers. The group has also a strong track record in training young scientists that have been incorporated to industrial laboratories and academia.
Facilities for numerical simulation
Hardware: Linux cluster (192 cores/320GB RAM), supercomputer SUN Fire X2200 (1264 computing cores, 3 TB RAM memory, 24 TB of shared storage); supercomputer Alhambra (1808 cores (3616 threads), 4.28 TB RAM memory, 72 TB shared storage).
Software: Home-made nanoscale device simulation suite, 1D Schrödinger-Poisson solver for CV and tunneling gate current calculation, and ab-initio SIESTA and Quantum Expresso for devices based on 2D semiconductors. Synopsys TCAD suite.
Facilities for electrical and structural characterization
100 m2 laboratory equipped with AFM, XPS spectroscopy, Raman microspectrometer; high-resolution SEM and TEM microscopes; semiautomatic 300 mm probe stations; manual Cryogenic Probe Station (4.5K-450K) with magnetic capability up to 0.3T; pseudo-MOSFET characterization set-up; noise characterization system; semiconductor analyzers for IV, CV measurements; impedance analyzer 40Hz-110MHz; PNA-X network analyzer (10MHz-26.5GHz).
Facilities for fabrication
A 20m2 class 1000 clean room hosts the lithography equipment, a direct laser writing system with a resolution of 0.1um and two lasers, one of 375nm and a second one of 266nm. The rest of equipment for TMDs fabrication is placed in a class 10000 clean room with 120m2. A PVD deposition system is used for metal deposition. The system allows the deposition up to metallic layers by thermal evaporation and/or e-beam evaporation without breaking the vacuum. An oxidation furnace for the thermal growth of SiO2 (wet, dry and steam) is available. The growth of 2D-materials is performed in a CVD furnace with two quartz tubes to avoid cross contamination (Planartech). Graphene, hBN, and major TMDs (transition metal dichalcogenides) can be grown. A Reactive Ion Etching system with Ar, SF6 and CF4 is used to etch the deposited layers and resists. An O2 plasma cleaner and an ozone cleaner are also available for surface treatment.
3) Aquatic biogeochemistry laboratory (Reche´s team). This laboratory is dedicated to the characterization of dissolved and particulate organic matter and greenhouse gases. It is equipped with: a Shimadzu TOC-V-CSH Organic Total Carbon Analyzer with TNM-1 coupled nitrogen module; a Perkin-Elmer UV-VIS LAMBDA 45 spectrophotometer (+UV WinLab 5 software); a spectrofluorometer JY-Horiba Spex Fluoromax-4; a Picarro CRDS Analyzer (G2508) to measure in quasi-continuous and simultaneous mode the flows of greenhouse gases (CO2, CH4, N2O); a Seabird 19plus CTD profiler coupled to Spherical Underwater Quantum Sensor (LI-193R); and a fluorimeter Turner® SCUFA (model CYCLOPS–7), sediment traps, and several filtration and sampling devices. Recently, Reche and Rueda´s team have installed a floating platform for continuous recording and interpretation of greenhouse gas emissions including a Eddy Covariance tower (Licor LI-7500DS Open Path CO2/H2O and Licor LI7700 Open Path CH4), submergible probes for dissolved CH4 (CONTROS HydroCTM CH4), temperature profiles, oxygen profiles (TriOS DO), chlorophyll a (Nano-Flu), CO2 profiles (ATM), and CDOM (Nano-Flu).
4) Microbial Ecology laboratory (Reche´s team). This laboratory is dedicated to the characterization (structure and function) of the microorganisms existing in the aquatic ecosystems and the atmosphere. It is equipped with a Becton Dickinson FACScalibur flow cytometer (CIC-UGR); Eppendorf PCR mastercycler; Eppendorf Refrigerated Microcentrifuge 5415; electrophoresis systems; and Q-PCR systems (CIC-UGR).
5) Genetics Molecular laboratory (Perfectti’s team). The Evolutionary Genetics Laboratory is dedicated to the use of molecular genetics techniques to study population genetics, genomics, and evolution. It includes DNA/RNA extraction mills; a liquid management robot; several PCRs and a shared q-PCR; refrigerated and micro-centrifuges; a DNA spectrophotometer; several electrophoretic systems; a gel-documentation system; autoclave, ovens, binocular loupes and microscopes, including a fluorescent microscope with CCD-refrigerated camera; refrigerators and freezers, including a -80C ultra freezer. To process genomic data, the laboratory maintains a 48-threads two-cores server with 512 GB of RAM and 12 TB hard disk space, along with two disk servers with 20 + 10 TB of backup and storage space.
6) Experimental greenhouse and chambers for plants (teams led by Perfectti, Gómez, and Rubio). It includes a new experimental greenhouse with four separate modules with independent climatic control, an additional greenhouse of smaller capacity, and an area for common-garden experiments. It also includes a plant growing room with eight growing chambers (phytotrons) of different capacities.
7) The Ultrasonics laboratory hosts leading edge ultrasonic equipment for laboratory research in broad biomedical applications: imaging, scanning and biomechanical characterization of complex materials and tissue. It is widely recognized as one of the top facilities worldwide. The devices are listed below along with their main features. A high-speed ultrasound scanner to monitor the viscoelastic properties and functional imaging of soft tissue and tissue-mimicking materials (Verasonics): it consists of three systems (server, generator and PC) with frequencies ranging from 2 – 42 MHz (high frequency) and 0.5 – 1.5 MHz (low frequency) with amplitudes from 2 to 190 Vpp; an immersion water tank CNC-scanner for ultrasonic scanning of materials, used with a set of transducers from 50 KHz to 100 MHz. It scans up to 1000mm with a resolution down to 10 μm, and digitizes down to the picosecond with 14 bits depth; moreover, the laboratory hosts a unique ultrasonic scanner designed specifically for nonlinear ultrasonic measurements (harmonic generation technique), including CNC system (accuracy < 1mm), calibration system, immersion system, transmission transducers (0.1-10 MHz and 60 Vpp), acquisition and digitization system; it also hosts a unique torsional wave scanner designed specifically for linear and nonlinear torsional ultrasound monitoring of soft tissue, including robotic positioning (accuracy < 1mm), calibration system, transducer (0.2-4 KHz and 20 Vpp), pressure control, acquisition and digitization; as for classical ultrasound systems, it hosts 9 wave generators with frequencies from 1 μHz to 250 MHz up to 10V, 6 Oscilloscopes up to 350 MHz and 4GSsa/s, 4 AR amplifiers up to 150W from 10 KHz to 100Mhz, 3 additional portable systems, 3 clinical echographs, 2 of them with elastography; furthermore, the laboratory hosts a laser interferometer with a digitization with accuracy less than 10mm/s/V, up to 2,5 Mhz; a contact-free ultrasonic equipment, including transducers, acquisition and digitization, which allows for the manipulation of biological specimens avoiding their contamination (frequency of 0.1 – 1 MHz); 2 3D printers with different technologies and accuracies. One of them uses fused deposition modeling (FDM) to achieve an accuracy of 0.1 mm per layer, ranging polymers such as PLA, ABS, PCL, etc. The other one uses photopolymer biocompatible materials, with a spatial resolution of 14 microns; A GPU-based computing server (2 NVidia Titan V 12G Hbm2 and CPU Intel i9 4.2 GHz) for modeling cell-communications, ultrasonic interactions and tumor dynamics.
8) The Fluids and Biocoloids laboratory serves facilities for new materials and bio-engineering, hosting the following equipment: Rotavap+Extrusion rheometer; homogenizer, tribometer, torsional and capillary rheometer (home-made); high-speed cameras (Photron and Miro); (magneto)rheometer (Anton-Paar); spectrophotometer; Malvern PCS-4700; Photon Cross Correlation Spectroscopy 3DS; ALV-NIBS/HPPS; Zetameter Brookhaven ZetaPALS; Zetameter Malvern Zetasizer Nano Z; Nanoparticle Tracking Analysis (NTA)-NanoSight LM10-HS(GB) FT14 (NanoSight, Amesbury, United Kingdom); Langmuir balance and mini-trough; pendant drop tensiometer (home-made); dust-free romos; magnetowetting (home-made), sliding/rolling angle (third-party prototype); bouncing drop (home-made); microdrop dispenser (Thorlabs MLS203P+ Microdrop MD-E-3000); growing/shrinking sessile drop/captive bubble (home-made); AFM (Nanoscope IV, Veeco); WLCM (Plu, Sensofar); RF Plasma etcher (K1050X, Emitech); optical microscope (Phase Contrast-2, OPTIPHOT-2, Nikon); Direct Laser Patterning (POWERLINE E 20, ROFIN); pull-off tests (MH2-500N-FA + ZTA-200N and ZTA-20N, IMADA); abrasion and wear tests (Falling Sand Abrasion Tester, IBERTEST; 5750 Linear Abraser, TABER Industries); icing chamber (home-made), surface preparation/modification: dip-coating (FILMLIFT FL-1 E, LAUDA); spin-coating (WS-650MZ-23NPP/LITE, Laurrel Technologies corporation); polishing (Ecomet 250 + Automet 250, Buehler); UV/Ozone (PSD Pro Series, Novascan); sandblasting (Sandblast Cabinet-CAT990, MW-TOOLS).
9) Although in the different laboratories MNat has sophisticated computing services, as already mentioned, the Unit has access to the Computer and Communications Network Services Centre (CSIRC) at UGR, which has been supporting scientific research since 1990. This centre has the UGRGrid supercomputer, which is based on a distributed memory arquitecture and composed by a SUN Fire X2200 M2/X4600 M2 cluster with 1264 computing cores, a total of 3 TByte RAM memory, 24 TByte of shared storage and a high-performance Infiniband interconnection. Also, it includes Alhambra, which is a HPC system composed by Fujitsu PRIMERGY CX250/RX350/RX500 nodes and comprising 1808 cores (a total of 3616 threads), 4.28 TByte RAM memory, 72 TByte shared storage and QDR InfiniBand interconnection. MNat is connected to the Barcelona Supercomputing Center-National Supercomputing Center (BSC-CNS), which will house one of the next major supercomputers in Europe sponsored by the EC. The equipment has recently been extended to the Albaicín supercomputer, one of the 5 most powerful in Spain.