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Biological and Chemical Physics Commons™
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Full-Text Articles in Biological and Chemical Physics
Binding Of Solvated Peptide (Eplqlkm) With A Graphene Sheet Via Simulated Coarse-Grained Approach, Somayyeh Sheikholeslami, R. B. Pandey, Nadiya Dragneva, Wely Floriano, Oleg Rubel, Stephen A. Barr, Zhifeng Kuang, Rajiv Berry, Rajesh Naik, Barry Farmer
Binding Of Solvated Peptide (Eplqlkm) With A Graphene Sheet Via Simulated Coarse-Grained Approach, Somayyeh Sheikholeslami, R. B. Pandey, Nadiya Dragneva, Wely Floriano, Oleg Rubel, Stephen A. Barr, Zhifeng Kuang, Rajiv Berry, Rajesh Naik, Barry Farmer
Faculty Publications
Binding of a solvated peptide A1 (1E 2P 3L 4Q 5L 6K 7M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and …
Semiclassical Application Of The Mo/Ller Operators In Reactive Scattering, Sophya V. Garashchuk, J. C. Light
Semiclassical Application Of The Mo/Ller Operators In Reactive Scattering, Sophya V. Garashchuk, J. C. Light
Faculty Publications
Mo/ller operators in the formulation of reaction probabilities in terms of wave packet correlation functions allow us to define the wave packets in the interaction region rather than in the asymptotic region of the potential surface. We combine Mo/ller operators with the semiclassical propagator of Herman and Kluk. This does not involve further approximations and can be used with any initial value representation (IVR) semiclassical propagator. Time propagation in asymptotic regions of the potential due to Mo/ller operators reduces the oscillations of the propagator integrand and improves convergence of the results with respect to the number of trajectories. The effectiveness …
Simplified Calculation Of The Stability Matrix For Semiclassical Propagation, Sophya V. Garashchuk, J. C. Light
Simplified Calculation Of The Stability Matrix For Semiclassical Propagation, Sophya V. Garashchuk, J. C. Light
Faculty Publications
We present a simple method of calculation of the stability (monodromy) matrix that enters the widely used semiclassical propagator of Herman and Kluk and almost all other semiclassical propagators. The method is based on the unitarity of classical propagation and does not involve any approximations. The number of auxiliary differential equations per trajectory scales linearly rather than quadratically with the system size. Just the first derivatives of the potential surface are needed. The method is illustrated on the collinear H3 system.