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Full-Text Articles in Physics
Scaling And Alpha-Helix Regulation Of Protein Relaxation In A Lipid Bilayer, Liming Qiu, Creighton Buie, Kwan H. Cheng, Mark W. Vaughn
Scaling And Alpha-Helix Regulation Of Protein Relaxation In A Lipid Bilayer, Liming Qiu, Creighton Buie, Kwan H. Cheng, Mark W. Vaughn
Physics and Astronomy Faculty Research
Protein conformation and orientation in the lipid membrane plays a key role in many cellular processes. Here we use molecular dynamics simulation to investigate the relaxation and C-terminus diffusion of a model helical peptide: beta-amyloid (Aβ) in a lipid membrane.We observed that after the helical peptide was initially half-embedded in the extracelluar leaflet of phosphatidylcholine (PC) or PC/cholesterol (PC/CHOL) membrane, the C-terminus diffused across the membrane and anchored to PC headgroups of the cytofacial lipid leaflet. In some cases, the membrane insertion domain of the Aβ was observed to partially unfold. Applying a sigmoidal fit to the process, we found …
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 …
Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi
Structural Flexibility And Oxygen Diffusion Pathways In Monomeric Fluorescent Proteins, Chola K. Regmi
FIU Electronic Theses and Dissertations
Fluorescent proteins are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions …
Lattice Thermal Conductivity In Bulk And Nanosheet Naxcoo2, Denis Demchenko, David B. Ameen
Lattice Thermal Conductivity In Bulk And Nanosheet Naxcoo2, Denis Demchenko, David B. Ameen
Physics Publications
In this paper we present the results of calculations of the lattice thermal conductivity of layered complex metal oxide NaxCoO2 within the Green–Kubo theory. Using NaxCoO2 we identify the two competing mechanisms responsible for the favorable scaling properties of the Green–Kubo method for calculating the lattice thermal conductivity. The artificial correlations of the heat flux fluctuations due to the finite size of the supercells are partially cancelled by the missing long wavelength acoustic phonon modes. We compute the lattice thermoelectric properties of bulk NaxCoO2 with varying stoichiometry, structural defects, and temperature. …
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 …