Brad A. Bauer

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Molecular dynamics (MD) simulations are a vital tool in chemical research, as they are able to provide an atomistic view of chemical systems and processes that is not obtainable through experiment. However, large-scale MD simulations require access to multicore clusters or supercomputers that are not always available to all researchers. Recently, scientists(More)
We investigate permeation energetics of water entering a model dimyristoylphosphatidylcholine (DMPC) bilayer via molecular dynamics simulations using polarizable Charge Equilibration (CHEQ) models. Potentials of mean force show 4.5-5.5 kcal/mol barriers for water permeation into bilayers. Barriers are highest when water coordination within the bilayer is(More)
All-atom molecular dynamics simulations have been applied in the recent past to explore the free energetics underlying ion transport processes in biological ion channels. Roux and co-workers, Kuyucak and co-workers, Busath and co-workers, and others have performed rather elegant and extended time scale molecular dynamics simulations using current(More)
We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh(More)
[1] High-resolution temperature reconstructions (typically annually to seasonally resolved) have played a key role in understanding paleoclimate immediately prior to the beginning of the instrumental record, especially when calibrated to form an extension of comparable instrumental data coverage (global, hemispheric, and regional). Such calibration allows(More)
When studying membrane-bound protein receptors, it is necessary to move beyond the current state-of-the-art simulations that only consider small membrane patches and implicit solvent. Limits of traditional computer platforms negatively impact the model's level of realism and the computational scales achievable. On the other hand, multi-core platforms such(More)
Potentials of mean force for single, nonpolarizable monovalent halide anions and alkali cations are computed for transversing the water-air interface (modeling using polarizable TIP4P-FQ and TIP4P-QDP). Iodide and bromide in TIP4P-FQ show interfacial stability, whereas chloride, bromide, and iodide show interfacial stability in TIP4P-QDP. A monotonic(More)
The results of iterative Hirshfeld partitioning on the polarizability of monovalent anions (F(-), Cl(-), and Br(-)) and Na(+) in water clusters ranging from n = 0 to n = 25 are presented. In each case, the ions reach a limiting intrinsic polarizability in the fully hydrated state. For F(-), Cl(-), and Br(-) using B3LYP/aug-cc-pVDZ, the intrinsic(More)
N-Acetyl-β-glucosamine (NAG) is an important moiety of glycoproteins and is involved in many biological functions. However, conformational and dynamical properties of NAG molecules in aqueous solution, the most common biological environment, remain ambiguous due to limitations of experimental methods. Increasing efforts are made to probe structural(More)
With the continuing advances in computational hardware and novel force fields constructed using quantum mechanics, the outlook for non-additive force fields is promising. Our work in the past several years has demonstrated the utility of polarizable force fields, those based on the charge equilibration formalism, for a broad range of physical and(More)