Leandro Martínez

How Designed Liquids Are Revolutionizing Our Understanding of Proteins

cces.unicamp.br/how-designed...

How Noether’s Theorem Revolutionized Physics | Quanta Magazine Emmy Noether showed that fundamental physical laws are just a consequence of simple symmetries. A century later, her insights continue to shape physics.

“Before Noether’s theorem, the principle of conservation of energy was shrouded in mystery,” the physicist and mathematician Feza Gürsey wrote in 1983. “… Noether’s simple and profound mathematical formulation did much to demystify physics.”
https://buff.ly/414iuVL

Qual o papel do cientista na sociedade? YouTube video by TV Unicamp

Qual o papel do cientista na sociedade?
Com Ronaldo Aloise Pilli, IQ Unicamp, e José Mário Martínez, IMECC da Unicamp. Pilli e Martínez são membros da Academia Brasileira de Ciências (ABC).
www.youtube.com/watch?v=lf_X...
cc @lmiq.bsky.social

Osmolyte-Induced Structural and Thermodynamic Effects on the Protein Folding Landscape Understanding how osmolytes influence protein folding is fundamental in biology and biotechnology. We developed a computational pipeline to investigate the structural and thermodynamic effects of osmolytes across the protein folding landscape: Using coarse-grained simulations to generate folding ensembles, we then employed atomistic simulations to explore each conformation in aqueous solutions of urea and TMAO. Minimum-distance distribution functions and the Kirkwood-Buff solvation theory provide unprecedented details on the solvation structures and thermodynamics. We studied two model proteins: the β-sheet SH3 domain and the helical B domain of protein A (BdpA). Urea stabilizes most denatured states, while TMAO destabilizes them. However, urea destabilizes partially denatured states of BdpA, which are only marginally affected by TMAO, demonstrating that osmolytes can selectively interfere with denaturation pathways. We show that urea-induced denaturation arises from strengthened non-specific interactions in unfolded states, leading to increased protein dehydration. Cosolvent effects on folding free energies match experimental data within 1 kcal/mol, validating force-fields and analysis methods. These findings provide a novel perspective on osmolyte-protein interplay, with implications for solvent and biomolecular design. ### Competing Interest Statement The authors have declared no competing interest.

Transfer free energies of native and denatured states of proteins to urea and TMAO are computed. The reweighed stability affects folding pathways. This work is possible by using minimum distance distribution functions and the ComplexMixtures.jl package. #compchem #chemsky #julialang

Cation Hydrophobicity Effects on Protein Solvation in Aqueous Ionic Liquids This study examines the influence of cation hydrophobicity on protein solvation in aqueous solutions of Ionic Liquids. Ubiquitin solvation structures and thermodynamics in systems with 1-ethyl-3-methy...

New research online: understanding cation hydrophobic effects on protein solvation. Using ComplexMixtures.jl #compchem #julialang

chemrxiv.org/engage/chemr...

Molecular dynamics and solvation structures of the β-glucosidase from Humicola insolens (BGHI) in aqueous solutions containing glucose The β-glucosidase enzyme is a glycosyl hydrolase that breaks down the β-1,4 linkage of cellobiose. It is inhibited by glucose at high concentrations d…

New paper online. Here we use MD simulations and the ComplexMixtures.jl package to understand the relationship between solvation and activity of a glucosidase. #moleculardynamics #julialang

Sim

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Subject to: José Mario Martínez YouTube video by Subject to

Esse Martínez é o meu pai. Este aqui: youtu.be/Qe4c8AIZULw

A associação "comemora". Produtores canalhas e burros.

Aprosoja MT comemora aprovação de projeto contra moratória da soja | Agro Estadão Proposta impede a concessão de incentivos fiscais e terrenos públicos a empresas organizadas em acordos que restrinjam a competitividade do produto mato-grossense

"Na prática, a legislação acaba com a moratória da soja, um acordo que proíbe, desde 2008, a compra de grãos de áreas desmatadas da Amazônia e que atinge principalmente as empresas que comercializam o grão (tradings) especialmente para o mercado externo."

agro.estadao.com.br/agropolitica...

Lugar certo na hora certa. Tipo o Watson.

Os programas deveriam descrever eles mesmos a relevância do seu trabalho conjunto, dando os destaques que julgarem importantes. E isto deveria ser avaliado em vez de um monte de numerinhos. Seria muito mais interessante os programas competindo para ter algo realmente relevante para relatar.

Similar to what happens with minimum wage increases and distributive programs.

ETF de Argentina em NY é o melhor do mundo sob Milei; Brasil ocupa vice-lanterna Especialistas explicam os motivos do desempenho positivo dos hermanos - e contam se vale ou não a pena investir agora

Os delírios.

www.infomoney.com.br/onde-investi...

Argentina: inflação anual acelera e vai a 236,7% em agosto, enquanto país vive contração da economia; entenda Apesar da alta do setor agrícola e pecuário, o consumo e as principais indústrias do país continuem sofrendo com os impactos das medidas econômicas do presidente Javier Milei.

A realidade.

g1.globo.com/economia/not...

bsky.app/profile/uol....

Geospatial Software Development at Arpeggeo® Description We are seeking a highly skilled and motivated Software Engineer to join our team, focusing on the development of cutting-edge geospatial software solutions. The ideal candidate will have s...

Sharing an interesting job opportunity:

Julio Hoffimann, ceo of Arpeggeo, is among the lead developers of the Julia framework for geospacial research github.com/JuliaGeo.

GitHub - adolfont/caes005-introduction-to-functional-programming: CAES005 - Introdução à Programação Funcional CAES005 - Introdução à Programação Funcional. Contribute to adolfont/caes005-introduction-to-functional-programming development by creating an account on GitHub.

As inscrições em Introduction to Functional Programming estão abertas
github.com/adolfont/cae...

São todas criadas por Brasileiros? Que interessante.

Essas três têm relação entre si?

I confess sometimes I have to code in Python.

And suddenly my opinion that arxiv publications are the future begins to change. We might need, on the contrary, stricter peer review.

Jabuticabeira em flor

Notebook showing up Julia features for particle simulations. Units, error propagation, differentiability, and performance. Takes a bit to load because of some videos. With Pluto.jl. #julialang

m3g.github.io/2021_Fortran...

Acompanho o Fora da Política, e é excelente. Mas o seu microfone está bem ruim nos últimos episódios.

Subscribe – AntennaPod AntennaPod is a podcast player that is completely open. The app is open-source and you can subscribe to any RSS feed. AntennaPod is built by volunteers without commercial intere...

I follow Emilia's (and now this one) in AntennaPod which is Open Source :-) and, honestly, very nice for podcasts. (antennapod.org/deeplink/sub...).

As versões modernas de Fortran são interessantes, e há desenvolvimento ativo, em particular com um compilador interativo baseado em LLVM (LFortran). Acho que tem espaço sim, Rust é interessante mas acho que para computação numérica a sintaxe atrapalha. Eu, particularmente, só estou usando Julia.

Na verdade Packmol é 100% Fortran. Tem um script em TCL no repositório mas não é realmente usado.

Hoje em dia só estou usando Julia mesmo, inclusive para uma nova versão do Packmol.