Benjamin G. Levine

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The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for(More)
The M2 proton channel from influenza A virus is an essential protein that mediates transport of protons across the viral envelope. This protein has a single transmembrane helix, which tetramerizes into the active channel. At the heart of the conduction mechanism is the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the(More)
Influenza A viruses are highly pathogenic and pose an unpredictable public health danger to humans. An attractive target for developing new antiviral drugs is the PA N-terminal domain (PAN) of influenza polymerase, which is responsible for the endonuclease activity and essential for viral replication. Recently, the crystal structures of the holo form of PAN(More)
The computational design of advanced materials based on surfactant self-assembly without ever stepping foot in the laboratory is an important goal, but there are significant barriers to this approach, because of the limited spatial and temporal scales accessible by computer simulations. In this paper, we report our work to bridge the gap between laboratory(More)
The A/M2 protein of influenza A virus forms a tetrameric proton-selective pH-gated ion channel. The H(37)xxxW(41) motif located in the channel pore is responsible for its gating and proton selectivity. Channel activation most likely involves protonation of the H37 residues, while the conductive state of the channel is characterized by two or three charged(More)
The tetrameric M2 protein bundle of the influenza A virus is the proton channel responsible for the acidification of the viral interior, a key step in the infection cycle. Selective proton transport is achieved by successive protonation of the conserved histidine amino acids at position 37. A recent X-ray structure of the tetrameric transmembrane (TM)(More)
The calculation of radial distribution functions (RDFs) from molecular dynamics trajectory data is a common and computationally expensive analysis task. The rate limiting step in the calculation of the RDF is building a histogram of the distance between atom pairs in each trajectory frame. Here we present an implementation of this histogramming scheme for(More)
We demonstrate that though exact in principle, the expansion of the total molecular wave function as a sum over adiabatic Born-Oppenheimer (BO) vibronic states makes inclusion of the second-derivative nonadiabatic energy term near conical intersections practically problematic. In order to construct a well-behaved molecular wave function that has density at(More)
Spikes in the time-derivative coupling (TDC) near surface crossings make the accurate integration of the time-dependent Schrödinger equation in nonadiabatic molecular dynamics simulations a challenge. To address this issue, we present an approximation to the TDC based on a norm-preserving interpolation (NPI) of the adiabatic electronic wave functions within(More)
A hydrophobic theory is combined with a Debye-Hückel approximation to calculate surfactant micellization properties such as the critical micelle concentration (cmc) and concentration effects. The predictive power of the theory is validated by comparison with experimental data of various ionic surfactant types in presence of salt. The theory is also used to(More)