1 of 14

Recent advances in structural biology powered by artificial intelligence have enabled the rapid de novo design of novel protein binders. These breakthroughs are now widely applied to the discovery of ligands, peptides, and even proteins or miniproteins capable of regulating biological functions. Notably, these achievements were recognized by the Nobel Prize in Chemistry, awarded to David Baker for innovations in protein design, alongside Demis Hassabis and John Jumper for developing AI-based protein structure prediction methods. In this project, we have selected a bacterial kinase—recently identified as essential for bacterial growth—as our target, given the significant impact of bacterial infections on human health. We propose leveraging generative AI tools to discover new ligands, with a particular focus on developing peptides and miniproteins that can downregulate kinase activity. To achieve this, we will utilize state-of-the-art platforms such as BindCraft, RFDiffusion, and BoltzGen, among others, to design peptides and miniproteins capable of inhibiting the enzymatic activity of the target kinase. The resulting sequences will be synthesized as peptides or genes (for miniproteins) and evaluated for their ability to inhibit the enzyme in vitro. In parallel, our group is developing proprietary AI-based tools for structure-conditioned generation of small-molecule binders. These initiatives are part of our broader research program dedicated to advancing generative AI applications in structural biology.

3 of 14

��Black Carbon (BC), a major product of incomplete combustion, is both a potent climate forcer and a pervasive marine pollutant. Yet, its biological interactions remain largely unresolved. This project will study the effects and modifications of pollution particles on the human lung and on marine fauna and flora, especially zooplankton, using confocal scanning microscopy with two-photon (2P) excitation. This fluorescence imaging technique has proven very efficient for studying these nanoparticles in tissues and microorganisms in our laboratory. Although 2P microscopy has been applied to tissue analysis and BC detection in biomedical contexts, its potential for environmental imaging, particularly for tracing pollutant–zooplankton interactions, has remained unexplored.��

STUDY OF POLLUTION PARTICLES AND THEIR EFFECTS ON THE ENVIRONMENT

FRANCISCO EDUARDO GONTIJO GUIMARÃES

Currículo Lattes

4 of 14

In this project we will use heterologously expressed and purified complex carbohydrate-active enzymes to degrade microbial biofilms as a novel approach to combat antimicrobial resistance of pathogenic bacteria.��

� ENZYMATIC DEGRADATION OF COMPLEX CARBOHYDRATES AND ITS APPLICATIONS AGAINST ANTIMICROBIAL RESISTANCE

IGOR POLIKARPOV�Google Scholar

5 of 14

SYNTHESIS AND STRUCTURAL CHARACTERIZATION VIA SINGLE CRYSTAL X-RAY DIFFRACTION

�

JAVIER ALCIDES ELLENA�Google Scholar

Abstract: This project aims to introduce the student to the fundamental techniques of modern Structural Crystallography. The main focus will be the complete determination of the three-dimensional structure of an organic and inorganic compound using the Single-Crystal X-ray Diffraction (SCXRD) technique. The student will be involved in all stages of the process, from the synthesis and growth of quality crystals to data collection, solution and refinement of the structure, and critical analysis of the results. The project will not only provide a practical understanding of one of the most important techniques for material characterization, but will also solidify fundamental concepts of symmetry, chemical bonding, and the solid state�2. Introduction and Theoretical Basis: Understanding the physical and chemical properties of a material is intrinsically linked to knowledge of its atomic structure. Single-crystal X-ray diffraction is the "gold standard" tool for obtaining this information with picometric precision (10⁻¹² m).Key concepts the student will master:• Unit Cell and Space Group: The fundamental repeating unit of the crystal and its symmetry.• Structure Factor: The amplitude of the wave scattered by a set of planes.• Phase Problem: The central challenge in crystallography, solved by direct or molecular substitution methods.• Least Squares Refinement: The iterative process of fitting the atomic model to experimental data.

6 of 14

Main Objective: To determine and analyze the crystal structure of organic and inorganic compounds.Specific Objectives:1. To synthesize and optimize the conditions for the growth of a single, high-quality single crystal.2. To operate the single-crystal X-ray diffractometer: to select, mount, and center a suitable crystal.3. To collect a complete set of diffraction data.4. To solve the initial structure using direct methods.

5. Refine the structural model, including atomic coordinates, thermal vibration parameters, and occupancy.6. Critically analyze the resulting structure, identifying coordination geometries, bond distances and angles, and intermolecular interactions (e.g., hydrogen bonds, π-π stacking).7. Prepare a final report in the format of a short scientific paper, including crystallographic data tables and figures of the structure. At the end of this project, the undergraduate student will have:1. Acquired cutting-edge practical experience in an analytical technique crucial to Solid State Physics, Chemistry, and Materials Science.2. Developed a deep understanding of crystal symmetry and its relationship to material properties.3. Produced a complete set of crystallographic data for a new compound, which can be deposited in the Cambridge Structural Database (CSD), an international database.4. Developed transferable skills in problem-solving, critical data analysis, and written and oral scientific communication.

7 of 14

Nonlinear optics is an important research field where the ultrafast laser development brings tremendous advances. High peak intensity and time resolution are the two most important characteristic of ultrashort femtosecond laser pulses which play important role to study nonlinear optical phenomena. In this project we will explore how ultrashort pulses can be used to measure and understand the third-order nonlinear effects: the nonlinear refraction and absorption, using different techniques. These nonlinear effects are very important for photonics devices, such as optical switches, for example. However, such nonlinear effects can be from different origins which need to be known. In this context, it is important to pay attention in the origin of such processes and use appropriate measurement methods to discriminate them. In order to do so, it is important to know that the nonlinear refraction and absorption, n2 and B2, respectively, need to be expressed by third-order nonlinear susceptibility tensors. For most of the materials, there are two independent elements named coefficients A and B to represent the third-order nonlinear susceptibilities. �

NONLINEAR OPTICS WITH ULTRAFAST FEMTOSECOND PULSES

LINO MISOGUTI�Currículo Lattes

8 of 14

The ratio of these two coefficients depends of the nature of the physical process that produces the nonlinearity. For molecular orientation, B/A=6, nonresonant electronic response, B/A=1, or thermal nonlinearity, B/A=0. Also, different experimental techniques access differently these two coefficients. For example, the Z-scan technique using linear polarization or circular polarization, the signal depends of coefficients A and B, or coefficient A, respectively. This special polarization dependence can be used to determine the origin of the nonlinear process. In addition, the nonlinear ellipse rotation (NER) only measure the coefficient B. In summary, in this project different techniques are explored to achieve better understanding on nonlinear effects of different material such as glasses, crystals, semiconductors, solvents, etc. Basically, the student will work on fundamental understanding of nonlinear optical processes exploring different techniques such as the Z-scan, nonlinear microscopy and NER measurements with ultrafast femtosecond lasers. Since it is an ongoing experiment, the student will learn most of the skill working with other students.��

.�

9 of 14

REVEALING THE FIRST STEP OF IMMUNE CARGO SELECTION IN THE SECRETORY PATHWAY

LUIS FELIPE SANTOS MENDES�Google Scholar

Protein sorting in the early secretory pathway is a fundamental yet underappreciated aspect of eukaryotic cell biology. Members of the p24/TMED family act as selective cargo receptors at the ER–Golgi interface, regulating both anterograde transport and the retention of membrane proteins in the Golgi apparatus. Among these, TMED1 has emerged as a potential mediator of immune-related signalling, as in cell studies suggest that its luminal GOLD domain interacts with the TIR domain of the membrane receptor ST2L, a key component of the IL-33 inflammatory signalling axis. Despite this functional evidence, no structural or biophysical data exist to define how GOLD–Cargo recognition occurs or whether this interaction contributes to cargo selection and transport. Addressing this gap is essential for understanding how immunity-related receptors are trafficked and how TMED-mediated checkpoints could regulate inflammatory responses. This short project (2 months) aims to provide the visiting student with a hands-on introduction to protein expression, purification, and interaction analysis in the context of molecular biophysics and structural biology. The student will focus on reconstructing the minimal interaction system between TMED1-GOLD and ST2L-TIR in vitro.

10 of 14

The student will: (1) Clone different constructs of the soluble TIR domain, including full-length luminal regions and truncated variants, to improve stability. (2) Establish expression and purification protocols for these constructs using E. coli systems, affinity chromatography, and SEC, learning how to evaluate protein folding and homogeneity through SDS-PAGE, DLS, and circular dichroism. (3) Initiate interaction assays between purified TIR and the GOLD domain of TMED1 (already available in the host laboratory), using preliminary binding titrations. Given the short timeframe, the central goal is not to build a full structural model but to generate high-quality reagents and foundational experimental conditions for a long-term project. The student will gain a strong conceptual and practical foundation in protein biophysics, membrane-associated transport mechanisms, and structure-function relationships in immune receptors. This project will introduce the student to an active research environment at the São Carlos Institute of Physics (USP), providing training that bridges molecular biology, biochemical engineering, and structural biophysics.

11 of 14

Protozoa and giant viruses (Nucleocytoviricota) are among representatives of ancient organisms, close to the formation of the first eukaryotes. The Project aims to identify novel free-living protozoa and giant viruses (Nucleocytoviricota) in the natural environment and investigate their structure and biochemistry to contribute with the fundamental questiono of eukaryogenesis.

INVESTIGATION OF THE DIVERSITY OF PROTOZOA AND GIANT VIRUSES

OTAVIO HENRIQUE THIEMANN

Currículo Lattes

12 of 14

SUSTAINABLE SYNTHESIS OF FLEXIBLE GRAPHENE COMPOSITE SENSORS FOR DETECTING H2S AND SO2 GASES.

VALMOR ROBERTO MASTELARO�Currículo Lattes

The project aims to develop flexible laser-induced graphene (LIG) sensors for detecting H2S and SO2 gases. The laser-induced graphene (LIG) will be obtained from residual biomass of agro-industrial origin, especially those rich in aromatic and lignocellulosic structures. To enhance the catalytic power of the LIG, its modification with metallic nanoparticles and semiconductor oxides synthesized through a biogenic route (using extracts from renewable waste) is proposed.

13 of 14

EXPERIMENTS AND THEORY WITH BOSE-EINSTEIN CONDENSATION . EXPERIMENTS USING BIOPHOTONIC FOR CANCER AND MICROBIOLOGICAL CONTROL

VANDERLEI SALVADOR BAGNATO�Google Scholar

1) Bose-Einstein Condensation - Trapped cold atoms to investigate different aspect of quantum phases. In special, the investigation of Quantum Turbulence and relaxation of out of equilibrium system . Different stages of relaxation and universalities are presetn and in investigation.2) Biophotonics for cancer and microbiol control - Using photodynamic as the main mechanism to destroy cells and microorganisms , breaking down the resitance to antibiotic and treating infrection in general. Developmet of techniques, instrumentation and understanding mechanisms.

14 of 14

RESEARCH WITH BOSE-EINSTEIN CONDENSATE. QUANTUM TURBULENCE AND RELAXATION OF OUT OF EQUILIBRIUM QUANTUM SYSTEM

VANDERLEI SALVADOR BAGNATO�Google Scholar

Excitation of the trapped BEC can be done through a combination of fields that promote time distortion of the trapping potential. These excitations can evolve over time, promoting energy migration from the largest to the smallest scales in a process called cascade. We will perform temporal excitations that consist of deformation and slight rotation of the potential, causing the system to evolve to a turbulent regime. Simulations demonstrated generation of solitons, vortices and waves in the sample. Using time of flight techniques, we will measure the moment distribution, n(k, t) and from it we obtain the energy spectrum E (k, t). This makes it possible to identify the inertial regions, where E (k, t) is clearly dependent on the power law (inertial region) characteristic of turbulent regime, and to measure the energy flow migrating between the scales and their preservation from the absence of dissipation. The temporal evolution of the moment distribution allows to verify the presence of a space-time scalability, which indicate the presence of a class of universality in the phenomenon. The overall relaxation stages of a far from equilbirium system will be measured. For recent publication see PHYSICAL REVIEW LETTERS 134, 023401 (2025) and reference there in.