All-atom molecular dynamics simulation of protein translocation through an α-hemolysin nanopore

D Di Marino, EL Bonome, A Tramontano… - The journal of …, 2015 - ACS Publications
Nanopore sensing is attracting the attention of a large and varied scientific community. One
of the main issues in nanopore sensing is how to associate the measured current signals to …

The rate dependent response of a bistable chain at finite temperature

I Benichou, Y Zhang, OK Dudko, S Givli - … of the Mechanics and Physics of …, 2016 - Elsevier
We study the rate dependent response of a bistable chain subjected to thermal fluctuations.
The study is motivated by the fact that the behavior of this model system is prototypical to a …

Thermodynamics of small systems with conformational transitions: The case of two-state freely jointed chains with extensible units

M Benedito, S Giordano - The Journal of Chemical Physics, 2018 - pubs.aip.org
Several experimental methods are usually applied for stretching single molecules and
provide valuable insights about the static and dynamic responses induced by externally …

Unfolding pathway and its identifiability in heterogeneous chains of bistable units

M Benedito, S Giordano - Physics Letters A, 2020 - Elsevier
We investigate the behavior of a chain of bistable units with an heterogeneous distribution of
energy jumps between the folded and unfolded states. For homogeneous chains, loaded by …

Rate-dependent force–extension models for single-molecule force spectroscopy experiments

M Benedito, F Manca, PL Palla, S Giordano - Physical Biology, 2020 - iopscience.iop.org
Single-molecule force spectroscopy techniques allow for the measurement of several static
and dynamic features of macromolecules of biological origin. In particular, atomic force …

Driven diffusion against electrostatic or effective energy barrier across α-hemolysin

P Ansalone, M Chinappi, L Rondoni… - The Journal of Chemical …, 2015 - pubs.aip.org
We analyze the translocation of a charged particle across an α-Hemolysin (αHL) pore in the
framework of a driven diffusion over an extended energy barrier generated by the electrical …

Relevance of the speed and direction of pulling in simple modular proteins

CA Plata, ZN Scholl, PE Marszalek… - Journal of Chemical …, 2018 - ACS Publications
A theoretical framework capable of predicting the first unit that unfolds in pulled modular
proteins has been recently introduced, for “fast enough” pulling velocities. Within this picture …

Modelling the unfolding pathway of biomolecules: theoretical approach and experimental prospect

CA Plata, A Prados - Workshop on Coupled Mathematical Models for …, 2016 - Springer
We analyse the unfolding pathway of biomolecules comprising several independent
modules in pulling experiments. In a recently proposed model, a critical velocity v_ c has …

[CITATION][C] Relevance of the Speed and Direction of Pulling in Simple Modular Proteins

CA Plata Ramos, ZN Scholl… - … , 14 (6), 2910 …, 2018 - American Chemical Society