Hugh Nymeyer

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It is commonly known that the amino acid residue tryptophan and its side-chain analogs, e.g., indole, are strongly attracted to the interfacial region of lipid bilayers. Phenylalanine and its side-chain analogs, e.g., benzene, do not localize in the interface but are distributed throughout the lipid bilayer. We use molecular dynamics to investigate the(More)
Replica exchange molecular dynamics (REMD) has become a standard technique for accelerating relaxation in biosimulations. Despite its widespread use, questions remain about its efficiency compared with conventional, constant temperature molecular dynamics (MD). An analytic approach is taken to describe the relative efficiency of REMD with respect to MD.(More)
Experiments with fast folding proteins are beginning to address the relationship between collapse and folding. We investigate how different scenarios for folding can arise depending on whether the folding and collapse transitions are concurrent or whether a nonspecific collapse precedes folding. Many earlier studies have focused on the limit in which(More)
Replica exchange simulations are used to study the energy landscape of trpzip2, a model beta-hairpin system, using the AMBER99sb force field and explicit solvent. The total simulation time is 300 ns per replica (approximately 10 mus total). The trp side chains are observed to adopt multiple packing arrangements with a freezing temperature below 273 K in the(More)
Continuum electrostatic models have had quantitative success in describing electrostatic-mediated phenomena on atomistic scales; however, there continues to be significant disagreement about how to assign dielectric constants in mixed, nonhomogeneous systems. We introduce a method for determining a position-dependent dielectric profile from molecular(More)
A recent workshop titled "Quantitative Computational Biophysics" at Florida State University provided an overview of the state of the art in quantitative modeling of biomolecular systems. The presentations covered a wide range of interrelated topics, including the development and validation of force fields, the modeling of protein-protein interactions, the(More)
We present a new approach to parallelization of important scientific applications. It is based on the observation that results of prior, related, simulations are often available. We use such data to parallelize the time domain. We demonstrate the effectiveness of our approach in Molecular Dynamics (MD) simulations, which are widely used in nano and nano-bio(More)
Molecular dynamics is a popular technique to simulate the behavior of physical systems, with resolution at the atomic scale. One of its limitations is that an enormous computational effort is required to simulate to realistic time spans. Conventional parallelization strategies have limited effectiveness in dealing with this difficulty. We recently(More)
Serial tempering is a computational method that turns the temperature T (or more generally any independent λ parameter) into a dynamical variable. It is shown that, under conditions for which this variable is fast, serial tempering is equivalent to the umbrella sampling method with a single effective potential. This equivalence is demonstrated using both a(More)
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