Projects

Mechanical properties of silk

Silk is one of the many biomaterials with mechanical properties not yet reached by synthetic counterparts. Silk fibers have an outstanding toughness, that is, are very extensible while also sustaining large forces. They are exclusively made from protein in a way similar to a block-copolymer: blocks of polyalanine, assembled into stacks of beta-sheets representing nano-sized…

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Mechanical properties of Nacre

Nacre, also known as mother-of-pearl, is a biocomposite located at the inner layer of seashells, with exceptional mechanical properties such as fracture resistance, toughness and strength. Although its constituents are brittle CaCO3 crystals and ductile biomolecules, the combined structure exhibits extraordinary stiffness and toughness. Currently, artificial nacre-like composites are among the most promising materials for…

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Force-triggered blood coagulation

Blood coagulation is a complex phenomenon requiring the activation of a series of proteins upon changes in the physiological flow of blood inside blood vessels. The von Willebrand Factor is majorly involved in blood coagulation by a mechanism that is only partially known. Force acting on the protein upon changes in blood shear flow cause a…

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Structure-based Drug design

Structure-based design methods have proven effective in every aspect of drug design – from lead discovery, development, through guiding clinical trials. These methods may be used to optimise the  binding affinity of the drug candidate, to finely tune  the specificity of protein-ligand interactions, and for predictive in silico toxicology (off-target binding, CYP450 binding and metabolism). In the group,…

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Force-driven allostery in proteins

Allostery in proteins plays a significant role such as cell signalling or gene and enzyme regulations. Allostery is characterized by a signal propagation through single proteins or complexes. The signal is triggered by external forces or ligand binding and then propagated toward a distant site which could be several nanometers away. Experimental techniques usually fails…

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Mechano(bio)chemistry

Chemical and enzymatic reactions can be guided by mechanical stress. While single molecule force spectroscopy is an emerging technique to study biochemistry under external forces, theoretical knowledge to rationalize or predict the force dependency of reactions rates is limited to simple models. We are examining the effect of force on the electronic and molecular structures…

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Force distribution analysis (FDA)

Force distribution analysis (FDA) is a method to detect and follow force and stress propagation in proteins, reminiscent of Finite Element Analysis used to engineer macroscopic structures. The method is based on Molecular Dynamics simulations during which we directly calculate forces between each atom pair in a system. The most recent version of FDA is…

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