Zobrazeno 1 - 10
of 101
pro vyhledávání: '"Brotzakis, P."'
Autor:
Tribello, Gareth A., Bonomi, Massimiliano, Bussi, Giovanni, Camilloni, Carlo, Armstrong, Blake I., Arsiccio, Andrea, Aureli, Simone, Ballabio, Federico, Bernetti, Mattia, Bonati, Luigi, Brookes, Samuel G. H., Brotzakis, Z. Faidon, Capelli, Riccardo, Ceriotti, Michele, Chan, Kam-Tung, Cossio, Pilar, Dasetty, Siva, Donadio, Davide, Ensing, Bernd, Ferguson, Andrew L., Fraux, Guillaume, Gale, Julian D., Gervasio, Francesco Luigi, Giorgino, Toni, Herringer, Nicholas S. M., Hocky, Glen M., Hoff, Samuel E., Invernizzi, Michele, Languin-Cattöen, Olivier, Leone, Vanessa, Limongelli, Vittorio, Lopez-Acevedo, Olga, Marinelli, Fabrizio, Martinez, Pedro Febrer, Masetti, Matteo, Mehdi, Shams, Michaelides, Angelos, Murtada, Mhd Hussein, Parrinello, Michele, Piaggi, Pablo M., Pietropaolo, Adriana, Pietrucci, Fabio, Pipolo, Silvio, Pritchard, Claire, Raiteri, Paolo, Raniolo, Stefano, Rapetti, Daniele, Rizzi, Valerio, Rydzewski, Jakub, Salvalaglio, Matteo, Schran, Christoph, Seal, Aniruddha, Zadeh, Armin Shayesteh, Silva, Tomás F. D., Spiwok, Vojtěch, Stirnemann, Guillaume, Sucerquia, Daniel, Tiwary, Pratyush, Valsson, Omar, Vendruscolo, Michele, Voth, Gregory A., White, Andrew D., Wu, Jiangbo
In computational physics, chemistry, and biology, the implementation of new techniques in a shared and open source software lowers barriers to entry and promotes rapid scientific progress. However, effectively training new software users presents sev
Externí odkaz:
http://arxiv.org/abs/2412.03595
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of interconversi
Externí odkaz:
http://arxiv.org/abs/2207.04558
Autor:
Z. Faidon Brotzakis
Publikováno v:
FEBS Open Bio, Vol 13, Iss 7, Pp 1193-1203 (2023)
Metadynamics electron microscopy metaInference (MEMMI) is an integrative structural biology method that enables a rapid and accurate characterization of protein structural dynamics at the atomic level and the error in the cryo‐EM experimental data,
Externí odkaz:
https://doaj.org/article/6978b0ecb1c24caea3dad53c067e81e5
From the point of view of statistical mechanics, a full characterisation of a molecular system requires the experimental determination of its possible states, their populations and the respective interconversion rates. Well-established methods can in
Externí odkaz:
http://arxiv.org/abs/2006.00868
Transition path sampling (TPS) is a powerful technique for investigating rare transitions, especially when the mechanism is unknown and one does not have access to the reaction coordinate. Straightforward application of TPS does not directly provide
Externí odkaz:
http://arxiv.org/abs/1907.04453
Many processes of scientific and technological interest are characterized by time scales that render their simulation impossible if one uses present day simulation capabilities. To overcome this challenge a variety of enhanced simulation methods has
Externí odkaz:
http://arxiv.org/abs/1902.08854
Autor:
Taniya Bhardwaj, Kundlik Gadhave, Shivani K. Kapuganti, Prateek Kumar, Zacharias Faidon Brotzakis, Kumar Udit Saumya, Namyashree Nayak, Ankur Kumar, Richa Joshi, Bodhidipra Mukherjee, Aparna Bhardwaj, Krishan Gopal Thakur, Neha Garg, Michele Vendruscolo, Rajanish Giri
Publikováno v:
Nature Communications, Vol 14, Iss 1, Pp 1-16 (2023)
Bhardwaj et al., have explored the proteomes of SARS-CoV and SARS-CoV-2, and have demonstrated the amyloid formation of viral proteins, in vitro, through diverse biophysical techniques.
Externí odkaz:
https://doaj.org/article/2c66476a47044cdbb6efc553451a9fce
Publikováno v:
Frontiers in Molecular Biosciences, Vol 10 (2023)
Parkinson’s disease is characterised by the deposition in the brain of amyloid aggregates of α-synuclein. The surfaces of these amyloid aggregates can catalyse the formation of new aggregates, giving rise to a positive feedback mechanism responsib
Externí odkaz:
https://doaj.org/article/b790c6f95fb74fe99a38cf76ceda6bf8
Many processes of scientific importance are characterized by time scales that extend far beyond the reach of standard simulation techniques. To circumvent this impediment a plethora of enhanced sampling methods has been developed. One important class
Externí odkaz:
http://arxiv.org/abs/1808.07895
Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters are calibrated to reproduce properties measured by experiments or simul
Externí odkaz:
http://arxiv.org/abs/1804.02742