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List of works by Alessandro Barducci

Accuracy of current all-atom force-fields in modeling protein disordered states

scientific article published on 18 December 2014

Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 kDa Enzyme by Specific 1H-13C Labeling and Fast Magic-Angle Spinning NMR

scientific article published on 05 July 2019

Assessing the Quality of the OPEP Coarse-Grained Force Field

scientific article published on 19 May 2011

Behavior of polarizable models in presence of strong electric fields. I. Origin of nonlinear effects in water point-charge systems

scientific article published on 01 November 2005

Catch bond drives stator mechanosensitivity in the bacterial flagellar motor.

scientific article

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins.

scientific article

Combining metadynamics simulation and experiments to characterize dendrimers in solution

Communication: Role of explicit water models in the helix folding/unfolding processes

scientific article published in September 2016

Crooks equation for steered molecular dynamics using a Nosé-Hoover thermostat.

scientific article published in October 2006

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

scientific article published on 01 July 2019

Effect of the Synaptic Plasma Membrane on the Stability of the Amyloid Precursor Protein Homodimer.

scientific article

Effect of urea on the β-hairpin conformational ensemble and protein denaturation mechanism.

scientific article

Efficient conversion of chemical energy into mechanical work by Hsp70 chaperones

scientific article published on 17 December 2019

Emerging fields in chaperone proteins: A French workshop

article

Evolution of an intricate J-protein network driving protein disaggregation in eukaryotes.

scientific article

Free-energy landscape of protein oligomerization from atomistic simulations

scientific article

Function, evolution, and structure of J-domain proteins

scientific article published on 26 November 2018

Generalization of the Jarzynski and Crooks nonequilibrium work theorems in molecular dynamics simulations.

scientific article published on 7 May 2007

Hsp70 chaperones are non-equilibrium machines that achieve ultra-affinity by energy consumption

scientific article

Insights into the activation mechanism of human estrogen-related receptor γ by environmental endocrine disruptors

scientific article published on 24 May 2019

Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression

scientific article published on 06 June 2019

Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

scientific article (publication date: June 2015)

Linking well-tempered metadynamics simulations with experiments.

scientific article published on May 2010

Metadynamics simulation of prion protein: beta-structure stability and the early stages of misfolding

scientific article published in March 2006

Modeling Hsp70/Hsp40 interaction by multi-scale molecular simulations and coevolutionary sequence analysis

scientific article

Multiple routes and milestones in the folding of HIV-1 protease monomer

scientific article

Non-equilibrium conformational dynamics in the function of molecular chaperones.

scientific article published on February 2015

Nucleation of Biomolecular Condensates from Finite-Sized Simulations

scientific article published in 2023

Numerical verification of the generalized Crooks nonequilibrium work theorem for non-Hamiltonian molecular dynamics simulations.

scientific article published in July 2007

Prion protein β2-α2 loop conformational landscape

scientific article published on 21 August 2017

Probing the mechanism of pH-induced large-scale conformational changes in dengue virus envelope protein using atomistic simulations

scientific article

Quantifying the role of chaperones in protein translocation by computational modeling

scientific article published on 23 March 2015

Reconstructing the equilibrium Boltzmann distribution from well-tempered metadynamics.

scientific article published in August 2009

Recovering the Crooks equation for dynamical systems in the isothermal-isobaric ensemble: a strategy based on the equations of motion

scientific article published in January 2007

Replica Temperatures for Uniform Exchange and Efficient Roundtrip Times in Explicit Solvent Parallel Tempering Simulations

scientific article published on 22 June 2011

Self-healing umbrella sampling: a non-equilibrium approach for quantitative free energy calculations

scientific article published on 01 July 2006

Single-molecule spectroscopy reveals chaperone-mediated expansion of substrate protein

scientific article

Structural and energetic basis for hybridization limits in high-density DNA monolayers

scientific article published in 2013

Structural basis for chemically-induced homodimerization of a single domain antibody

scientific article published in Scientific Reports

Tackling sampling challenges in biomolecular simulations

scientific article published in January 2015

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

scientific article published on 23 April 2014

Theoretical and experimental characterization of amino-PEG-phosphonate-terminated Polyphosphorhydrazone dendrimers: Influence of size and PEG capping on cytotoxicity profiles

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

scientific article