Brad A. Bauer

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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)
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)
Combining umbrella sampling molecular dynamics (MD) simulations, the weighted histogram analysis method (WHAM) for unbiasing probabilities, and polarizable charge equilibration force fields, we compute the potential of mean force for the reversible transfer of methyl guanidinium from bulk solution to the center of a model DPPC bilayer. A 5 kcal/mol minimum(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)
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 activities of phosphofructokinase, aldolase and pyruvate kinase were diminished in extracts from skeletal muscle of streptozotocin diabetic rats, whereas the activities of glucose phosphate isomerase and phosphoglucomutase were not changed. Treatment of diabetic rats with insulin restored the activity of phosphofructokinase to normal. A kinetic study of(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)
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)
[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)