Noah S. Bieler

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The Cartesian Tensor Transfer Method (CTTM) was proposed as an efficient way to calculate infrared, Raman, and Raman Optical Activity (ROA) spectra for large molecules from the Hessian matrix and property tensor derivatives calculated for smaller molecular fragments. Although this approach has been widely used, its reliability has not been analyzed in depth(More)
The pre-fibrillar stages of amyloid formation have been implicated in cellular toxicity, but have proved to be challenging to study directly in experiments and simulations. Rational strategies to suppress the formation of toxic amyloid oligomers require a better understanding of the mechanisms by which they are generated. We report Dynamical Monte Carlo(More)
When using molecular dynamics (MD) simulations for the calculation of alchemical free-energy changes, the extended-dynamics method called λ-dynamics (λD) in its currently available implementations does not compare very favorably with thermodynamic integration (TI) in terms of robustness, efficiency, and accuracy, although it is in principle easier to set(More)
In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme,(More)
Estimating the relative stabilities of different conformational states of a (bio-)molecule using molecular dynamics simulations involves two challenging problems: the conceptual problem of how to define the states of interest and the technical problem of how to properly sample these states, along with achieving a sufficient number of interconversion(More)
An extension of the λ-local-elevation umbrella-sampling (λ-LEUS) scheme [ Bieler et al. J. Chem. Theory Comput. 2014 , 10 , 3006 ] is proposed to handle the multistate (MS) situation, i.e. the calculation of the relative free energies of multiple physical states based on a single simulation. The key element of the MS-λ-LEUS approach is to use a single(More)
In a recent article (Bieler et al., J. Chem. Theory Comput. 2014, 10, 3006), we introduced a combination of λ-dynamics and local-elevation umbrella-sampling termed λ-LEUS to calculate free-energy changes associated with alchemical processes using molecular dynamics simulations. This method was suggested to be more efficient than thermodynamic integration(More)
An algorithm is proposed for performing molecular dynamics (MD) simulations of a biomolecular solute represented at atomistic resolution surrounded by a surface layer of atomistic fine-grained (FG) solvent molecules within a bulk represented by coarse-grained (CG) solvent beads. The method, called flexible boundaries for multiresolution solvation (FBMS), is(More)
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