相关论文: Extending fragment-based free energy calculations …
The absolute free energy -- or partition function, equivalently -- of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule…
There is significant interest in rapid protein simulations because of the time-scale limitations of all-atom methods. Exploiting the low cost and great availability of computer memory, we report a Monte Carlo technique for incorporating…
We propose a new Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
The molecular distributions obtained from canonical Monte Carlo simulations can be used to find an approximate interaction energy. This serves as the basis of a method for estimating the binding free energy for a ligand to a protein which…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
We adapted existing polymer growth strategies for equilibrium sampling of peptides described by modern atomistic forcefields with implicit solvent. The main novel feature of our approach is the use of pre-calculated statistical libraries of…
We present a method to generate realistic, three-dimensional networks of crosslinked semiflexible polymers. The free energy of these networks is obtained from the force-extension characteristics of the individual polymers and their…
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries…
We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from…
Monte Carlo simulations are used to study the conformational properties of a folded semiflexible polymer confined to a long channel. We measure the variation in the conformational free energy with respect to the end-to-end distance of the…
We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to…
The crystallisation of entangled polymers from their melt is investigated using computer simulation with a coarse-grained model. Using hybrid Monte Carlo simulations enables us to probe the behaviour of long polymer chains. We identify…
We demonstrate the application of artificial neural network (ANN) models to reverse Monte Carlo based thermodynamic calculations. Adsorption isotherms are generated for 2D square and triangular lattices. These lattices are considered…
We present an efficient Monte-Carlo method for long-range interacting systems to calculate free energy as a function of an order parameter. In this method, a variant of the Wang-Landau method regarding the order parameter is combined with…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
In this paper, I investigate more closely the recently proposed Free Energy Monte Carlo algorithm that is devised in particular for calculations where conventional Monte Carlo simulations struggle with ergodicity problems. The simplest…
An efficient approach of measuring the absolute free energy in parallel tempering Monte Carlo using the exponential averaging method is discussed and the results are compared with those of population annealing Monte Carlo using the…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…