相关论文: Free Energy Calculations of Membrane Permeation: C…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
A new simulated tempering method, which is referred to as simulated tempering umbrella sampling, for calculating the free energy of chemical reactions is proposed. First principles molecular dynamics simulations with this simulated…
Major efforts in recent years have been directed towards understanding molecular transport in polymeric membranes, in particular reverse osmosis and nanofiltration membranes. Transition-state theory is an increasingly common approach to…
Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of powerful and flexible path…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
Alchemical free energy calculations are a useful tool for predicting free energy differences associated with the transfer of molecules from one environment to another. The hallmark of these methods is the use of "bridging" potential energy…
It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few hundred ns) in all-atom molecular dynamics(MD) simulations because the time required for the translocation of…
Free energy calculations in molecular simulations have a variety of applications including determining the strength of molecular processes such as solvation and binding. It has been recently shown that when removing the VDW and Coulomb…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
We use a simple and efficient computer model to investigate the physical properties of bilayer membranes. The amphiphilic molecules are modeled as short rigid trimers with finite range pair interactions between them. The pair potentials…
We present a simulation scheme to calculate defect formation free energies at a molecular crystal/water interface based on force-field molecular dynamics (MD) simulations. To this end we adopt and modify existing approaches to calculate…
The oxidation of human sebum, a lipid mixture covering our skin, generates a range of volatile and semi-volatile carbonyl compounds that contribute largely to indoor air pollution in crowded environments. Kinetic models have been developed…
We revisit the Fokker-Planck based theory of driven polymer translocation through a narrow nanopore. A bead-spring model of a uniformly charged polyelectrolyte chain translocating through a semi-implicit model of a nanopore embedded in a…
Recent progress in simulation methodologies and in computer power allow first principle simulations of condensed systems with Born-Oppenheimer electronic energies obtained by Quantum Monte Carlo methods. Computing free energies and…
We present an Adaptively Biased Molecular Dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using non-equilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling…
Free energies of molecules can be calculated by quantum computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic…
Free energies are fundamental quantities governing phase behavior and thermodynamic stability in polymer systems, yet their accurate computation often requires extensive simulations and post-processing techniques such as the Bennett…
In experiments, the free energy of transferring the peptide group from water to an osmolyte solution is obtained using the transfer free energy of (Gly)_n with the added assumption that a constant incremental change in free energy with n…