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Open Access Publications from the University of California

Scholarly Works (21 results)

  • Article
Lawrence Berkeley National Laboratory (2003)
    Cover page: Azimuthal Asymmetry of J/psi Suppression In Non-central Heavy-ion Collisions
    • Thesis
    • Peer Reviewed
    UC Irvine Electronic Theses and Dissertations (2014)

    Femtosecond two-dimensional infrared spectroscopy in combination with isotope labeling and molecular dynamics simulation has been used to investigate the structures and dynamics of nonfolding peptides and collagen peptides.

    Homopolymeric peptides are simple yet important, serve as model systems for investigating the intrinsic propensity of protein folding, especially for those disordered or unfolded peptides in aqueous solution. Here the full structure of (Ala)5 has been studied. Two different isotope-labeled peptides, Ala-(13C)Ala-(13C,18O)Ala-Ala-Ala, and Ala-Ala-(13C,18O)Ala-(13C)Ala-Ala were strategically designed to simplify the four-oscillator system into three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, coupling constant β and angle θ between transition dipoles has been extracted through spectral fitting. The coupling constant is around 4 cm-1 and angle around 100. These parameters were related to the dihedral angles characterizing the peptide backbone structure through DFT calculated maps. The derived dihedrals are all located in the polyproline-II region.

    These results were compared to the conformations sampled by hamiltonian replica-exchange MD simulation with 3 different CHARMM force fields: C22, C36 and Drude. The C22 force field predicted too high α-helix population, whereas C36 predicted that polyproline-II is the dominate conformation, consistent with experimental findings. The Drude model predicted dominating beta-sheet. Since the 2D-IR derived results were obtained from fitting to a single set of structural parameters, the effect of structural fluctuation within one conformation and structural transition between different conformations was also discussed. The C36 MD trajectories were used to simulate 2D IR spectra using the sum-over-state method and the time-averaging approximation (TAA) method. Reasonable agreement with the experimental data was achieved.

    Collagen is the most abundant protein in mammal. Its structural properties are important for biological functions. Here, the structure and thermal melting of a model collagen peptide, (PPG)10, has been investigated. The temperature dependent linear IR spectra of the unlabeled peptide and two isotopomers (either 13C-16O or 13C-18O labeled on the 4th glycine residue) showed that the triple helix unravels with increasing temperature and leads to greater solvent exposure. With some adjustments of calculation parameters according to linear IR spectra, 2D IR spectral simulation based on MD trajectories and TAA reasonably reproduced experimental spectra taken at the parallel and perpendicular polarization conditions. Further refinement of models and parameters are needed to improve the simulation. Our results for model nonfolding peptides and collagen peptides contribute to the fundamental understanding of peptide structure and dynamics, and to the further development of theoretical models for simulating 2D IR spectra.

      Cover page: Two-dimensional infrared spectroscopy of model peptides
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2017)
      We devised a novel two-step reference scheme that can greatly suppress the additive and convolutional noises in heterodyne nonlinear spectroscopy. To optimally remove additive noise, we fully utilized the spectral correlation in multi-channel reference data through a linear combination and regression algorithm. Using our pump-probe 2D IR spectrometer, we demonstrated that our scheme can improve the signal-to-noise ratio by 10-30 times and reach the noise floor of the signal detector. The new algorithm is guaranteed to reduce noise, enables the use of unmatched reference detectors, and does not introduce baseline shift or signal distortion. This scheme is applicable to many heterodyne spectroscopic techniques.
        • Article
        • Peer Reviewed
        UC Irvine Previously Published Works (2019)
        In this work, we optimize and further advance a noise reduction scheme for heterodyne spectroscopy. This scheme linearly combines data from reference detectors to predict the noise statistics in the signal detector through an optimized coefficient matrix. We validate this scheme for visible white-light-continuum and 800-nm light sources using un-matched CMOS arrays and show that the signal-to-noise ratio can approach the noise floor of the signal detector while using only ~5% of the energy for reference detection. We also optimize the strategy for estimating the coefficient matrix in practical applications. When combined with elaborate algorithms to perform pixel data compression and expansion, our scheme is applicable in difficult situations, including when the sample position is rapidly scanned, when detectors exhibit nonlinear response, and/or when laser fluctuations are large. The scheme is generalized to scenarios with complex chopping or phase cycling patterns, and a simple approach is provided for the chopping case. Finally, a robust and computationally efficient method is devised to remove multiplicative noise.
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2021)
          Presented here is a modular methodology for time-domain stochastic seismic wave propagation analysis. Presented methodology is designed to analyse uncertain seismic motions as an input, propagating through uncertain material. Traditional approach for uncertain wave propagation relies on models that include deep bedrock, local soil site, and their random process and random field information. Such models can become quite large and computationally intractable. The modular approach proposed herein features two step approach that allows separate consideration of the deep bedrock and local site along with corresponding random field information. The first step considers an auxiliary stochastic motions problem in the bedrock. Stochastic local site response can then be simulated in a reduced domain within certain depth from the surface. Application of uncertain seismic motions at depth, for local uncertain site response is done using stochastic effective forces developed through the Domain Reduction Method. By using Hermite polynomial chaos expansion to represent the non-Gaussian random field of material parameters and non-stationary random process of seismic motion, the proposed modular methodology is formulated using intrusive stochastic Galerkin approach, as seen in the Stochastic Elastic–Plastic Finite Element Method (SEPFEM). Developed modular methodology is illustrated using a 1-D stochastic seismic wave propagation analysis with three cases, and simulation results are also verified with results from conventional approach.
            Cover page: A modular methodology for time-domain stochastic seismic wave propagation
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2022)
            Modeling of Fourier amplitude spectra (FAS) of seismic motions has gained much attention in engineering seismology. In the past few years, several ground motion prediction equations (GMPEs) and inter-frequency correlation structure of FAS have been established. Due to many preferable characteristics of FAS, probabilistic seismic hazard/risk analysis is rapidly changing from ergodic, spectrum acceleration Sa(T0)-based approach to non-ergodic, site-specific, FAS-based approach. This paper presents time domain intrusive framework for probabilistic seismic risk analysis using GMPE of FAS. Methodology for time domain stochastic ground motion modeling based on GMPEs of FAS is presented in some detail. The simulated uncertain motions are modeled as a random process and represented by polynomial chaos Karhunen-Loève expansion. The random process excitations are further propagated into the uncertain structural system using Galerkin stochastic finite element method (SFEM). Probabilistic evolution of structural response is solved, and such solution is used to develop seismic risk for any damage state. The presented framework is illustrated through seismic risk analysis of a four-story building subjected to possible earthquakes from two strike slip faults. The influences of the epistemic uncertainties in source stress drop Δσ and site attenuation κ0 on seismic risk are investigated. The need for non-ergodic seismic risk analysis with source-specific and site specific characterizations is emphasized.
              Cover page: Time domain probabilistic seismic risk analysis using ground motion prediction equations of Fourier amplitude spectraCreative Commons 'BY-NC' version 4.0 license
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2021)
              Presented is an application of wave potential formulation (WPF) together with domain reduction method (DRM) to modeling earthquake soil structure interaction (ESSI) behavior in horizontally layered ground under inclined incident seismic waves. Wave potential formulation is used to develop a spatially varying, inclined seismic wave field from incident Primary (P) and Secondary (S) waves that propagate through layered ground. Developed seismic wave field is then used to develop effective forces for Domain Reduction Method that are then used for analyzing ESSI response of a soil structure system. Developed methodology, called WPF-DRM, is verified using analytic solution for a free field response of layered ground subjected to inclined incident waves. Developed WPF-DRM methodology is illustrated through analysis of an ESSI response of a deeply embedded structure, a small modular reactor (SMR) subjected to incident S wave polarized in vertical plane (SV) with variation in inclinations and frequencies. Presented example highlights the influences of incident wave inclination and frequency on ESSI response of analyzed SMR.
                Cover page: Modeling and simulation of earthquake soil structure interaction excited by inclined seismic waves
                • Article
                • Peer Reviewed
                UC Irvine Previously Published Works (2021)
                Enkephalins are small opioid peptides whose binding conformations are catalyzed by phospholipid membranes. Binding to opioid receptors is determined by the orientation of tyrosine and phenylalanine side chains. In this work, we investigate the effects of different charged phospholipid headgroups on the insertion of the tyrosine side chain into a lipid bilayer using a combination of 2D IR spectroscopy, anharmonic DFT calculations, and third order response function modeling. The insertion is probed by using the ∼1515 cm-1 tyrosine ring breathing mode, which we found exhibits rich vibrational dynamics on the picosecond timescale. These dynamics include rapid intramolecular vibrational energy redistribution (IVR), where some of the energy ends up in a dark state that shows up as an anharmonically shifted combination band. The waiting-time dependent 2D IR spectra also show an unusual line shape distortion that affects the extraction of the frequency-frequency correlation function (FFCF), which is the dynamic observable of interest that reflects the tyrosine side chain's insertion into the lipid bilayer. We proposed three models to account for this distortion: a hot-state exchange model, a local environment dependent IVR model, and a coherence transfer model. A qualitative analysis of these models suggests that the local environment dependent IVR rate best explains the line shape distortion, while the coherence transfer model best reproduced the effects on the FFCF. Even with these complex dynamics, we found that the tyrosine ring mode's FFCF is qualitatively correlated with the degree of insertion expected from the different phospholipid headgroups.
                  Cover page: Ultrafast vibrational dynamics of the tyrosine ring mode and its application to enkephalin insertion into phospholipid membranes as probed by two-dimensional infrared spectroscopy
                  • Article
                  • Peer Reviewed
                  UC Irvine Previously Published Works (2016)
                  We have studied the structure of (Ala)5, a model unfolded peptide, using a combination of 2D IR spectroscopy and molecular dynamics (MD) simulation. Two different isotopomers, each bis-labeled with (13)C═O and (13)C═(18)O, were strategically designed to shift individual site frequencies and uncouple neighboring amide-I' modes. 2D IR spectra taken under the double-crossed ⟨π/4, -π/4, Y, Z⟩ polarization show that the labeled four-oscillator systems can be approximated by three two-oscillator systems. By utilizing the different polarization dependence of diagonal and cross peaks, we extracted the coupling constants and angles between three pairs of amide-I' transition dipoles through spectral fitting. These parameters were related to the peptide backbone dihedral angles through DFT calculated maps. The derived dihedral angles are all located in the polyproline-II (ppII) region of the Ramachandran plot. These results were compared to the conformations sampled by Hamiltonian replica-exchange MD simulations with three different CHARMM force fields. The C36 force field predicted that ppII is the dominant conformation, consistent with the experimental findings, whereas C22/CMAP predicted similar population for α+, β, and ppII, and the polarizable Drude-2013 predicted dominating β structure. Spectral simulation based on MD representative conformations and structure ensembles demonstrated the need to include multiple 2D spectral features, especially the cross-peak intensity ratio and shape, in structure determination. Using 2D reference spectra defined by the C36 structure ensemble, the best spectral simulation is achieved with nearly 100% ppII population, although the agreement with the experimental cross-peak intensity ratio is still insufficient. The dependence of population determination on the choice of reference structures/spectra and the current limitations on theoretical modeling relating peptide structures to spectral parameters are discussed. Compared with the previous results on alanine based oligopeptides, the dihedral angles of our fitted structure, and the most populated ppII structure from the C36 simulation are in good agreement with those suggesting a major ppII population. Our results provide further support for the importance of ppII conformation in the ensemble of unfolded peptides.
                    Cover page: Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2018)
                    Presented is an energy dissipation analysis framework for granular material that is based on thermodynamics. Theoretical formulations are derived from the second law of thermodynamics, in conjunction with a few plausible assumptions on energy transformation and dissipation. The role of plastic free energy is emphasized by a conceptual experiment showing its physical nature. Theoretical formulation is adapted in order to be applied in elastic–plastic finite element method (FEM) simulations. Developed methodology is verified through comparison of input work, stored energy, and energy dissipation of the system. Separation of plastic work into plastic free energy and energy dissipation removes a common mistake, made in a number of publications, where energy dissipation can attain negative values (energy production) which is impossible.
                      Cover page: Energy dissipation analysis of elastic–plastic materials
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