LQMC/CIBFar: “New mechanisms to accelerate drug discovery for Neglected Tropical Diseases (NTDs)”

The Drugs for Neglected Diseases initiative (DNDi) is a patient-needs driven, not-for-profit research and development (R&D) organization that develops safe, effective, and affordable medicines for the millions of neglected patients across the world. DNDi focuses on developing new treatments for the most neglected patients suffering from diseases such as human African trypanosomiasis (sleeping sickness), leishmaniasis, Chagas disease, filariasis, paediatric HIV, mycetoma, and hepatitis C. The initiative’s primary objective is to deliver a total of 16 to 18 treatments by 2023 and to establish a strong R&D portfolio for these diseases. The R&D strategies developed by DNDi since its inception aim to address the immediate needs of patients by improving existing therapeutic options in the short term, whilst undertaking longer term research to identify and develop entirely new compounds which will be valuable adapted tools, particularly for elimination targets set by the World Health Organization. In 2013, DNDi began building a new consortium in Latin America (LOLA), providing support and mentoring for young scientists in the region. The consortia conduct hit-to-lead and lead optimization activities for visceral leishmaniasis and Chagas disease via a decentralized virtual model, and the talk focus will be the innovative R&D model and the efforts aiming at strengthening research capacities in the region. Jadel Kratz joined DNDi in June 2016 as Lead Optimization Latin America Coordinator focused in drug discovery projects in the region. He supports both the global and local R&D teams, and promotes the expansion of a regional consortia of scientific partners. Prior to joining DNDi, Dr. Kratz participated and coordinated academic research projects across various areas. Recently, he worked as R&D Coordinator at Cristália, a Brazilian-based pharmaceutical company. Dr Kratz is a pharmacist, and earned his PhD in Pharmaceutical Sciences (2011) at the Universidade Federal de Santa Catarina, Florianópolis, Brazil, with a visiting researcher period at the Uppsala University, Sweden. He completed postdoctoral fellowships at the University of Innsbruck and the University of Vienna, Austria.

LQMC/CIBFar: “Advances in Ligand-based and Structure-based Drug Design Software”

In recent years we have seen a rise in the use of computer-aided drug design tools in pharmaceutical companies as a result of advances in the underlying methods coupled with vast increases in computational resources. Here, we present an overview of the tools in the Schrödinger Suites, including ligand-based and structure-based approaches. We show that improvements in the underlying force field can improve results across a broad range of applications. We also show that molecular dynamics simulations can be used to accurately predict protein conformational states and protein-ligand binding free energies. Woody Sherman is Vice President of Applications Science at Schrödinger. He received his B.S. in Physical Chemistry from the University of California at Santa Barbara where he studied nonlinear optical properties of organic polymers using computational quantum mechanics. He completed his Ph.D. at MIT working in Professor Bruce Tidor’s lab where he examined the role of electrostatics in protein-ligand binding and implemented a novel method for optimizing ligand binding specificity across a panel of targets. While in graduate school he completed an internship at Biogen where he helped develop novel methods to enhance antibody affinity through electrostatic charge optimization, resulting in a publication and patent. At Schrödinger, he is involved in applications projects, product development, methods development, and scientific software support. He also works closely with customers on research projects and collaborations. Woody has published on a broad range of topics, including induced-fit docking, ensemble docking, protein design, small molecule optimization, cheminformatics, hybrid ligand/structure-based methods, free energy simulations, charge optimization, pharmacophore modeling, and more. He is a reviewer for top journals in computational chemistry and drug design and is on the Editorial Board of both Chemical Biology & Drug Design and Journal of Chemical Information and Modeling.

LQMC/CIBFar: “Residue Coevolution via Direct Coupling Analysis”

Faruck Morcos is an assistant professor in the Department of Biological Sciences and Department of Bioengineering at the University of Texas at Dallas. He is also member of the Center for Systems Biology at UT Dallas. Before starting his lab at UT Dallas, he was a postdoctoral fellow at the Center for Theoretical Biological Physics, first at the University of California San Diego and later at Rice University. He received his Ph.D. in Computer Science (Computational Biology) from the University of Notre Dame. He also holds a M.S. in Electrical Engineering from the Technical University of Munich and a M.S. in Applied Mathematics from Notre Dame. He has a B.S. (Honors) in Electronics and Communications Engineering from ITESM Campus Monterrey. In 2010, he received the Research Excellence Award given by the Computer Science Department at the University of Notre Dame. In 2005, the Kellogg Institute for International Studies awarded him the Kellogg Fellowship for Graduate Studies at the University of Notre Dame and in 2002 he received the Werner von Siemens Excellence Award to pursue graduate studies in Germany. His research focuses on applications of information theory, statistical inference and physical modeling to study molecular structure, function and interactions. His current interests include molecular coevolution and the analysis of biological information to study disease.

LQMC/CIBFar: “Biopharmaceuticals: Myth vs. Facts”

– What is a pharmaceutical (small molecule vs biologic), innovative, branded, generic product?

– Relative market sizes and evolution over time: market sizes by type, by geographies, by therapeutic area (by sales);

– Top biopharma players; some key products (noticeable breakthroughs rather than simply size);

– Increase in number of companies and products under development (in numbers and by therapeutic area) has been large;

– However, only a small number is approved each year;

– And the cost of developing a drug has increased significantly;

– Industry R&D productivity has been in serious decline for years;

– But opportunities for successful products still exist…

– What does it take to develop a product?

– Tunnel charts: show how long it takes to develop a drug (pre-competitive and competitive spaces);

– Approval rates and costs by phase (and by therapeutic area?);

– Product lifecycle;

– Characterization of industry segments;

– Forces of change: overview of strategic.

Filosofísica: “Desculpe o transtorno, mas precisamos conversar sobre mecânica bohmiana”

As interpretações que lhe contaram de mecanica quântica são realmente as que saem dos experimentos? Ou mesmo as que saem dos postulados formais da teoria? Que argumentos descartaram a possibilidade de uma interpretação causal para a mecânica quântica na época em que a controversia ainda tinha lugar entre os principais pesquisadores da área, marginalizando todas as tentativas posteriores de formular descrições não probabilísticas (não causais) de processos quânticos? A mecânica bohmiana, resultado dos trabalho de David Bohm nos anos 50, é atualmente mencionada por físicos quase sempre como uma curiosidade histórica e não como uma alternativa teórica de fato, sendo subestimada e amplamente ignorada por esses. Nesse Filosofísica, o nosso queridíssimo filosofísico Iago Israel, vai nos explicar (bem do começo) o que a teoria de Bohm tem de diferente, interessante e como ela tenta contornar alguns aspectos problemáticos (para alguns) da interpretação usual, puramente probabilística.

Vejamos se ainda têm sentido hoje as indagações de John Bell que, para alguns, já teria colocado um ponto final nessas questões: “Por que será que a visão da onda piloto está ignorada nos livros de mecânica quântica? Não seria o caso de ensiná-la, não como a via única, mas como um antídoto a autossatisfação vigente?”

High-Energy Physics Seminars: “Hydrodynamics with polarization”

Using the Lagrangian hydrodynamic approach [1] we derive the ideal hydrodynamic limit of a fluid with a net polarization of the microscopic degrees of freedom. We discuss the relevance of this dynamics in the light of the experimental study of Hadron (Lambda and vector meson) polarization and other spin-dependent observables in heavy ion collisions, and conclude that our approach is the first term in an effective theory expansion appropriate to study these phenomena quantitatively.

[1] D.Montenegro, G.Torrieri, PRD, in press, arXiv:1604.05291

Hydrodynamics with polarization

AGUARDE A PROGRAMAÇÃO

IFSC OSA Student Chapter: “Professor Eric Van Stryland seminars”

We from IFSC OSA Student Chapter have the honour to receive Prof. Eric Van Stryland as part of the Travelling Lecturer program of the Optical Society. Prof. Stryland will give two seminars, a brief one about the history of The Optical Society and other pointing out fundamental aspects of his cutting-edge research. You are welcome to attend both seminars that will be held at Sala F-210 (Administration building) at 2 p.m of November 11th. Take a look below for further information about Prof. Stryland and the seminars.

History of The Optical Society (OSA)

I’ll give a brief introduction of how OSA began in 1916 and how it has turned into an international professional home for nearly 20,000 scientists and engineers. Its offerings are highly respected international refereed journals along with international conferences on optics and photonics. However, it is also a professional network for students and professionals to interact, develop careers in optics and photonics, and much more. It is my professional home and should become yours.

Nonlinear spectroscopy: absorption and refraction

At high optical irradiance of short pulse lasers, the absorption and refraction of materials changes temporarily. We have been developing nonlinear spectroscopic tools for measuring these changes of nonlinear absorption (NLA) and nonlinear refraction (NLR). The tools include Z-scan that separately yields the sign and magnitude of both NLA and NLR, pump-probe for the dynamics of NLA, and our newly developed Beam-Deflection technique that gives the dynamics of NLR. This last technique is so sensitive that it can measure the nonlinear refraction of air (λ/20,000 induced phase change). I will also discuss the interesting and intuitive relations between NLR and NLA determined by causality (nonlinear Kramers-Kronig relations). This leads to a discussion of nondegenerate nonlinearities, e.g. 2-photon absorption (2PA) with two different energy photons. We find orders of magnitude enhancement of 2PA for photon energy rations of ~10. We then utilize these nonlinearities for devices including gated IR detection with uncooled wide-gap semiconductors for 3D LIDAR and the possibility of a 2-photon laser.

l

“Measurement of leptonic cosmic rays with AMS-02, interpretation in terms of dark matter and pulsar”

Over the last two decades, there has been a strong interest in the cosmic ray positron fraction which exhibit an excess of high energy positrons whose origin is still highly uncertain. The Alpha Magnetic Spectrometer (AMS-02) is a general purpose high-energy particle physics detector operational on the International Space Station since May 2011. During its unique long duration mission AMS-02 is collecting large amount of data to study the behaviour of cosmic ray electrons and positrons with unprecedented precision. The latest measurements of positron fraction, positron flux and electron flux with AMS-02 will benpresented. The interpretation of the positron excess in terms of pulsar or dark matter will be presented in this talk.

Filosofísica: “Mais um breve passeio pela Filosofia contemporânea da Matemática”

Nesse seminário, o membro do grupo de estudos Uirá Matos prosseguirá nos guiando em incursão pelos territórios da Filosofia da Matemática, em uma continuação do seu panorama das mais atuais (ou nem tanto) questões do campo.

AGUARDE A PROGRAMAÇÃO

Filosofísica: “Os ‘raios N’ de René Blondlot: uma anomalia (na história) da ciência”

O físico francês René Prospet Blondlot (1849-1930) fez grandes trabalhos. Seus estudos para medir a velocidade de ondas hertzianas (eletromagnéticas) são bastante originais, obtendo o valor de 298.000 Km/s experimentalmente. René Blondlot ganhou vários prêmios da Academia de Ciência de Paris.

No começo do século XX o nosso personagem rincipal começa a estudar as características dos raios X, recém-descobertos, e em 1903 divulga seus achados sobre uma nova radiação, os “raios N”. Essa descoberta fez sucesso, uma nova área da física nasceu, houve trabalhos aplicando os raios N ao estudo do sistema nervoso. Em 1905 a maioria dos físicos, incluindo revistas científicas, concluiu que essa radiação não existia.

Os argumentos contrários à existência dessa radiação se baseavam na suposição de que René e outros viam o que queriam ver, por autossugestão. O que é esquecido é que Blondlot respondeu a essas críticas seriamente, com evidências fotográficas. Mesmo assim o assunto morreu. Essa apresentação tem por objetivo adentrar essa rica história e analisar os argumentos e evidências da época. Há ainda muitos mistérios sobre esse estranho episódio.

High-Energy Physics: “Scattering Amplitudes: from theoretical considerations to LHC applications”

The Feynman rules appear as a simple way to calculate scattering amplitudes, however some complications appear if the multiplicity of particles is large. For example, in the 2 to 2 scattering of gluons there are only 4 Feynman diagrams but if we add two extra gluons it grows to 220 diagrams. In the 80’s Stephen Parke and Tomasz Taylor found an incredible way to simplify the calculation of some classes of n-gluons scattering amplitudes based on helicity arguments. Since then, a lot of progress has been made on improving the amplitude techniques and on the understanding of the S-matrix physics. After a review of the spinor helicity formalism and some well known results based on it, I will discuss how we can use the helicity structure of scattering amplitudes in the SM and in the context of an effective Lagrangian description of BSM dynamics. The analysis reveals a novel set of helicity selection rules according to which, in the majority of 2 to 2 scattering processes at high energy, the SM and the leading BSM effects do not interfere. This have a big impact on how we should perform the EFT analysis and where we should search for new physics.

Seminários do Grupo de Óptica: “Optical spectroscopy and microscopy studies of biological objects”

Spectroscopic and microscopic techniques allow analysis of various aspects of biological systems on molecular level. One of the common problems of such studies is overlapping of absorption or fluorescence spectra of biological molecules of interest. Several examples of how to separate them are shown for in vitro and in vivo systems. These examples include analysis of competitive binding of two molecules (anticancer drugs, mutagens and biologically active substances) to nucleic acids via absorption spectroscopy, separation of fluorescence spectra of Photosystems via time-resolved fluorescence spectroscopy and microscopy and analysis of Forster Resonance Energy Transfer (FRET) between voltage-sensitive fluorescence proteins. As a result constants of binding of anticancer drugs and mutagens to nucleic acids are determined for molecules that absorb light in the same region with nucleic acids. Also composition and ratio of Photosystems is determined in leaves, which opens room for non-invasive “express” analysis of these parameters in plants, allowing determination of optimal growing conditions and presence of diseases. FRET studies of voltage sensitive fluorescent protein help to figure out the mechanism of its action and improve its functionality. In general, it is shown that number of different approaches can be used to analyze overlapping absorption and fluorescence spectra of biological molecules on different levels of organization in vitro and in vivo.

High-Energy Physics Seminars: “Vertex Functions and Bound States in Strongly Interacting Theories”

Protons and neutrons, the particles which make up the nuclei of atoms, are comprised of tiny constituents called quarks. Quantum chromodynamics (QCD) is a field theory which describes the so-called strong “colour” force, mediated by gluons, which binds the quarks together and is responsible for formation of nucleons and other objects, collectively known as hadrons. While there is ample experimental evidence that this theory is correct, there are certain phenomena related to hadrons which are not yet fully understood within the QCD framework. We attempt to elucidate some of these issues by studying QCD and similar models by means of the Dyson-Schwinger and Bethe-Salpeter (DS/BS) functional formalism. This approach allows one to work with the basic degrees of freedom of QCD, the quarks and gluons (which are not directly detectable in experiments, being eternally bound within hadrons), while at the same time giving access to physical observables like hadron masses and decay constants. We briefly discuss the main ideas behind the DS/BS framework, and give examples of its applications through an investigation of one of the fundamental interaction vertices in QCD, as well as a calculation of light hadron masses in a model similar to chromodynamics. Our findings help in building towards a better understanding of not just QCD but strongly-interacting theories in general, which is important since some of these templates play an important role in other areas of high-energy particle physics.

Seminário: “Recent advances in polymers from renewable resources”

 Research and development related to polymers from renewable resources have witnessed a spectacular development from the beginning of this millennium, with a progressively deeper and wider involvement of both academia and industry. This lecture aims at providing a succinct “state of the art” of this exciting field through a number of examples of recent advances, including contributions from my research groups. Two main approaches are discussed, namely: The chemical modification of natural polymers. This topic covers the synthesis and characterization of novel materials and composites arising from the surface, in-depth and bulk transformation of celulose fibers, including nanofibers, chitosan, starch, lignin and natural rubber. The synthesis and polymerization of monomers derived from renewable resources. The variety of such monomers and macromonomers has already reached a remarkably wide spectrum and is increasing incessantly. The examples provided in this context deal with small molecules derived from sugars and polysaccharides, lignin, and larger structures derived from vegetable oils. Particular emphasis is placed on furan monomers and furan chemistry, which provide a new class of polymer chemistry, including the application of structure-specific mechanisms like the Diels-Alder click reaction. Additionally, the peculiar properties of some of these new macromolecular materials, such as poly(lactic acid), other polyesters, polyamides and polyurethanes, are highlighted to show, among other features, their unique applications, e.g. recyclability and self-mendability.

Interessados em participar do seminário devem realizar inscrição por formulário on-line para previsão de público e envio de certificado de participação