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Parallel tempering: Theory, applications, and new perspectives
We review the history of the parallel tempering simulation method. From its origins in data
analysis, the parallel tempering method has become a standard workhorse of …
analysis, the parallel tempering method has become a standard workhorse of …
Effects of confinement on freezing and melting
We present a review of experimental, theoretical, and molecular simulation studies of
confinement effects on freezing and melting. We consider both simple and more complex …
confinement effects on freezing and melting. We consider both simple and more complex …
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 …
Multidimensional replica-exchange method for free-energy calculations
We have developed a new simulation algorithm for free-energy calculations. The method is
a multidimensional extension of the replica-exchange method. While pairs of replicas with …
a multidimensional extension of the replica-exchange method. While pairs of replicas with …
Electrostatic correlations: from plasma to biology
Electrostatic correlations play an important role in physics, chemistry and biology. In
plasmas they result in thermodynamic instability similar to the liquid–gas phase transition of …
plasmas they result in thermodynamic instability similar to the liquid–gas phase transition of …
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
Motivated by the protein structure prediction problem, we develop two variants of the
Hamiltonian replica exchange methods (REMs) for efficient configuration sampling,(1) the …
Hamiltonian replica exchange methods (REMs) for efficient configuration sampling,(1) the …
Generalized‐ensemble algorithms for molecular simulations of biopolymers
In complex systems with many degrees of freedom such as peptides and proteins, there
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …
exists a huge number of local‐minimum‐energy states. Conventional simulations in the …
Free-energy landscape for β hairpin folding from combined parallel tempering and metadynamics
We develope a new free-energy method, based on the combination of parallel tempering
and metadynamics, and apply this method to the calculation of the free-energy landscape of …
and metadynamics, and apply this method to the calculation of the free-energy landscape of …
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model
includes anisotropic potentials between bases involved in base stacking and base pair …
includes anisotropic potentials between bases involved in base stacking and base pair …
Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
In complex systems with many degrees of freedom such as spin glass and biomolecular
systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity …
systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity …