Mikolai Fajer

Learn More
A potential scaling version of simulated tempering is presented to efficiently sample configuration space in a localized region. The present "simulated scaling" method is developed with a Wang-Landau type of updating scheme in order to quickly flatten the distributions in the scaling parameter lambdam space. This proposal is meaningful for a broad range of(More)
Monitoring of exposure to 1,6-hexamethylene (HDI) monomers and HDI polyisocyanates in Oregon was initiated in 1980 and covered primarily spray painting and related activities. A total of 562 air samples were collected from 60 workplaces during the years 1980-1990 and analyzed for HDI and HDI polyisocyanate content. Of the total, only a small fraction (6%)(More)
Accelerated molecular dynamics (AMD) is an efficient strategy for accelerating the sampling of molecular dynamics simulations, and observable quantities such as free energies derived on the biased AMD potential can be reweighted to yield results consistent with the original, unmodified potential. In conventional AMD the reweighting procedure has an inherent(More)
Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling, compute reversible work and free energies, as well as refine transition pathways.(More)
Free energy governs the equilibrium extent of many biological processes. High barriers separating free energy minima often limit the sampling in molecular dynamics (MD) simulations, leading to inaccurate free energies. Here, we demonstrate enhanced sampling and improved free energy calculations, relative to conventional MD, using windowed accelerated MD(More)
In order to efficiently simulate spin label behavior when attached to the protein backbone we developed a novel approach that enhances local conformational sampling. The simulated scaling (SS) approach (Li, H., et al. J. Chem. Phys. 2007, 126, 24106) couples the random walk of a potential scaling parameter and molecular dynamics in the framework of hybrid(More)
We use thermodynamic integration (TI) and explicit solvent molecular dynamics (MD) simulation to estimate the absolute free energy of host-guest binding. In the unbound state, water molecules visit all of the internally accessible volume of the host, which is fully hydrated on all sides. Upon binding of an apolar guest, the toroidal host cavity is fully(More)
We explore a conformational transition of the TATTVGYG signature peptide of the KcsA ion selectivity filter and its GYG to AYA mutant from the conducting α-strand state into the nonconducting pII-like state using a novel technique for multidimensional optimization of transition path ensembles and free energy calculations. We find that the wild type peptide,(More)
This tutorial sets out to determine the free-energy difference between two conformational states of a short, terminally blocked peptide, N–acetyl–N –methylalaninamide, along a meaningful transition pathway. To reach this objective, use will be made of the string method with swarm of trajectories. Starting from a guess, rectilinear transition pathway(More)
Interpretation of EPR measurables from spin labels in terms of structure and dynamics requires knowledge of label behavior. General strategies were developed for simulation of labels used in EPR of proteins. The criteria for those simulations are (a) exhaustive sampling of rotamer space, (b) consensus of results independent of starting points, and (c)(More)