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Full-Text Articles in Physical Sciences and Mathematics
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 …
Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell
Low Mach Number Fluctuating Hydrodynamics Of Diffusively Mixing Fluids, Aleksandar Donev, Andy J. Nonaka, Yifei Sun, Thomas Fai, Alejandro Garcia, John B. Bell
Faculty Publications
We formulate low Mach number fluctuating hydrodynamic equations appropriate for modeling diffusive mixing in isothermal mixtures of fluids with different density and transport coefficients. These equations eliminate the fast isentropic fluctuations in pressure associated with the propagation of sound waves by replacing the equation of state with a local thermodynamic constraint. We demonstrate that the low Mach number model preserves the spatio-temporal spectrum of the slower diffusive fluctuations. We develop a strictly conservative finite-volume spatial discretization of the low Mach number fluctuating equations in both two and three dimensions. We construct several explicit Runge-Kutta temporal integrators that strictly maintain the …