[HTML][HTML] A guide to in silico drug design
The drug discovery process is a rocky path that is full of challenges, with the result that very
few candidates progress from hit compound to a commercially available product, often due …
few candidates progress from hit compound to a commercially available product, often due …
Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
Metadynamics is a powerful algorithm that can be used both for reconstructing the free
energy and for accelerating rare events in systems described by complex Hamiltonians, at …
energy and for accelerating rare events in systems described by complex Hamiltonians, at …
Transition path sampling and other advanced simulation techniques for rare events
Computer simulations of molecular processes such as nucleation in first-order phase
transitions or the folding of a protein are often complicated by widely disparate time scales …
transitions or the folding of a protein are often complicated by widely disparate time scales …
Adaptive biasing force method for scalar and vector free energy calculations
E Darve, D Rodríguez-Gómez… - The Journal of chemical …, 2008 - pubs.aip.org
In free energy calculations based on thermodynamic integration, it is necessary to compute
the derivatives of the free energy as a function of one (scalar case) or several (vector case) …
the derivatives of the free energy as a function of one (scalar case) or several (vector case) …
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
Recently, we have introduced a new method, metadynamics, which is able to sample rarely
occurring transitions and to reconstruct the free energy as a function of several variables …
occurring transitions and to reconstruct the free energy as a function of several variables …
Assessing the accuracy of metadynamics
Metadynamics is a powerful technique that has been successfully exploited to explore the
multidimensional free energy surface of complex polyatomic systems and predict transition …
multidimensional free energy surface of complex polyatomic systems and predict transition …
On-surface synthesis of unsaturated carbon nanostructures with regularly fused pentagon–heptagon pairs
Multiple fused pentagon–heptagon pairs are frequently found as defects at the grain
boundaries of the hexagonal graphene lattice and are suggested to have a fundamental …
boundaries of the hexagonal graphene lattice and are suggested to have a fundamental …
[BOOK][B] Advanced computer simulation approaches for soft matter sciences III
The series Advances in Polymer Science presents critical reviews of the present and future
trends in polymer and biopolymer science including chemistry, physical chemistry, physics …
trends in polymer and biopolymer science including chemistry, physical chemistry, physics …
Adaptively biased molecular dynamics for free energy calculations
We present an adaptively biased molecular dynamics (ABMD) method for the computation of
the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD …
the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD …
Simulation of structural phase transitions by metadynamics
We describe here in detail the recently introduced methodology for simulation of structural
transitions in crystals. The applications of the new scheme are illus trated on various kinds of …
transitions in crystals. The applications of the new scheme are illus trated on various kinds of …