Sensitivity analysis for calculating the risk of viral infection

Alessandro Cammarata,Giuliano Cammarata 한국지능시스템학회 2023 INTERNATIONAL JOURNAL of FUZZY LOGIC and INTELLIGE Vol.23 No.4

Application of principal component analysis and wavelet transform to fatigue crack detection in waveguides

Cammarata, Marcello,Rizzo, Piervincenzo,Dutta, Debaditya,Sohn, Hoon Techno-Press 2010 Smart Structures and Systems, An International Jou Vol.6 No.4

Ultrasonic Guided Waves (UGWs) are a useful tool in structural health monitoring (SHM) applications that can benefit from built-in transduction, moderately large inspection ranges and high sensitivity to small flaws. This paper describes a SHM method based on UGWs, discrete wavelet transform (DWT), and principal component analysis (PCA) able to detect and quantify the onset and propagation of fatigue cracks in structural waveguides. The method combines the advantages of guided wave signals processed through the DWT with the outcomes of selecting defect-sensitive features to perform a multivariate diagnosis of damage. This diagnosis is based on the PCA. The framework presented in this paper is applied to the detection of fatigue cracks in a steel beam. The probing hardware consists of a PXI platform that controls the generation and measurement of the ultrasonic signals by means of piezoelectric transducers made of Lead Zirconate Titanate. Although the approach is demonstrated in a beam test, it is argued that the proposed method is general and applicable to any structure that can sustain the propagation of UGWs.

Application of principal component analysis and wavelet transform to fatigue crack detection in waveguides

Marcello Cammarata,Piervincenzo Rizzo,Debaditya Dutta,손훈 국제구조공학회 2010 Smart Structures and Systems, An International Jou Vol.6 No.4

Ultrasonic Guided Waves (UGWs) are a useful tool in structural health monitoring (SHM) applications that can benefit from built-in transduction, moderately large inspection ranges and high sensitivity to small flaws. This paper describes a SHM method based on UGWs, discrete wavelet transform (DWT), and principal component analysis (PCA) able to detect and quantify the onset and propagation of fatigue cracks in structural waveguides. The method combines the advantages of guided wave signals processed through the DWT with the outcomes of selecting defect-sensitive features to perform a multivariate diagnosis of damage. This diagnosis is based on the PCA. The framework presented in this paper is applied to the detection of fatigue cracks in a steel beam. The probing hardware consists of a PXI platform that controls the generation and measurement of the ultrasonic signals by means of piezoelectric transducers made of Lead Zirconate Titanate. Although the approach is demonstrated in a beam test, it is argued that the proposed method is general and applicable to any structure that can sustain the propagation of UGWs.

Ultrafast Structural Dynamics of the Photocleavage of Protein Hybrid Nanoparticles

Ibrahimkutty, Shyjumon,Kim, Jangbae,Cammarata, Marco,Ewald, Friederike,Choi, Jungkweon,Ihee, Hyotcherl,Plech, Anton American Chemical Society 2011 ACS NANO Vol.5 No.5

<P>Protein-coated gold nanoparticles in suspension are excited by intense laser pulses to mimic the light-induced effect on biomolecules that occur in photothermal laser therapy with nanoparticles as photosensitizer. Ultrafast X-ray scattering employed to access the nanoscale structural modifications of the protein–nanoparticle hybrid reveals that the protein shell is expelled as a whole without denaturation at a laser fluence that coincides with the bubble formation threshold. In this ultrafast heating mediated by the nanoparticles, time-resolved scattering data show that proteins are not denatured in terms of secondary structure even at much higher temperatures than the static thermal denaturation temperature, probably because time is too short for the proteins to unfold and the temperature stimulus has vanished before this motion sets in. Consequently the laser pulse length has a strong influence on whether the end result is the ligand detachment (for example drug delivery) or biomaterial degradation.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancac3/2011/ancac3.2011.5.issue-5/nn200120e/production/images/medium/nn-2011-00120e_0007.eps'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/nn200120e'>ACS Electronic Supporting Info</A></P>

The Short-Lived Signaling State of the Photoactive Yellow Protein Photoreceptor Revealed by Combined Structural Probes

Ramachandran, Pradeep L.,Lovett, Janet E.,Carl, Patrick J.,Cammarata, Marco,Lee, Jae Hyuk,Jung, Yang Ouk,Ihee, Hyotcherl,Timmel, Christiane R.,van Thor, Jasper J. American Chemical Society 2011 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.133 No.24

<P>The signaling state of the photoactive yellow protein (PYP) photoreceptor is transiently developed via isomerization of its blue-light-absorbing chromophore. The associated structural rearrangements have large amplitude but, due to its transient nature and chemical exchange reactions that complicate NMR detection, its accurate three-dimensional structure in solution has been elusive. Here we report on direct structural observation of the transient signaling state by combining double electron electron resonance spectroscopy (DEER), NMR, and time-resolved pump–probe X-ray solution scattering (TR-SAXS/WAXS). Measurement of distance distributions for doubly spin-labeled photoreceptor constructs using DEER spectroscopy suggests that the signaling state is well ordered and shows that interspin-label distances change reversibly up to 19 Å upon illumination. The SAXS/WAXS difference signal for the signaling state relative to the ground state indicates the transient formation of an ordered and rearranged conformation, which has an increased radius of gyration, an increased maximum dimension, and a reduced excluded volume. Dynamical annealing calculations using the DEER derived long-range distance restraints in combination with short-range distance information from <SUP>1</SUP>H–<SUP>15</SUP>N HSQC perturbation spectroscopy give strong indication for a rearrangement that places part of the N-terminal domain in contact with the exposed chromophore binding cleft while the terminal residues extend away from the core. Time-resolved global structural information from pump–probe TR-SAXS/WAXS data supports this conformation and allows subsequent structural refinement that includes the combined energy terms from DEER, NMR, and SAXS/WAXS together. The resulting ensemble simultaneously satisfies all restraints, and the inclusion of TR-SAXS/WAXS effectively reduces the uncertainty arising from the possible spin-label orientations. The observations are essentially compatible with reduced folding of the I<SUB>2</SUB>′ state (also referred to as the ‘pB’ state) that is widely reported, but indicates it to be relatively ordered and rearranged. Furthermore, there is direct evidence for the repositioning of the N-terminal region in the I<SUB>2</SUB>′ state, which is structurally modeled by dynamical annealing and refinement calculations.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/2011/jacsat.2011.133.issue-24/ja200617t/production/images/medium/ja-2011-00617t_0002.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ja200617t'>ACS Electronic Supporting Info</A></P>

Spatiotemporal reaction kinetics of an ultrafast photoreaction pathway visualized by time-resolved liquid x-ray diffraction.

Kim, Tae Kyu,Lorenc, Maciej,Lee, Jae Hyuk,Lo Russo, Manuela,Kim, Joonghan,Cammarata, Marco,Kong, Qingyu,Noel, Sylvie,Plech, Anton,Wulff, Michael,Ihee, Hyotcherl National Academy of Sciences 2006 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.103 No.25

<P>We have studied the reaction dynamics for HgI(2) in methanol by using time-resolved x-ray diffraction (TRXD). Although numerous time-resolved spectroscopic studies have provided ample information about the early dynamics of HgI(2), a comprehensive reaction mechanism in the solution phase spanning from picoseconds up to microseconds has been lacking. Here we show that TRXD can provide this information directly and quantitatively. Picosecond optical pulses triggered the dissociation of HgI(2), and 100-ps-long x-ray pulses from a synchrotron probed the evolving structures over a wide temporal range. To theoretically explain the diffracted intensities, the structural signal from the solute, the local structure around the solute, and the hydrodynamics of bulk solvents were considered in the analysis. The results in this work demonstrate that the determination of transient states in solution is strongly correlated with solvent energetics, and TRXD can be used as an ultrafast calorimeter. It also is shown that a manifold of structural channels can be resolved at the same time if the measurements are accurate enough and that global analysis is applied. The rate coefficients for the reactions were obtained by fitting our model against the experimental data in one global fit including all q-values and time delays. The comparison between all putative reaction channels confirms that two-body dissociation is the dominant dissociation pathway. After this primary bond breakage, two parallel channels proceed. Transient HgI associates nongeminately with an iodine atom to form HgI(2), and I(2) is formed by nongeminate association of two iodine atoms.</P>

Photolysis of Br₂in CCl₄studied by time-resolved X-ray scattering

Kong, Qingyu,Lee, Jae Hyuk,Lo Russo, Manuela,Kim, Tae Kyu,Lorenc, Maciej,Cammarata, Marco,Bratos, Savo,Buslaps, Thomas,Honkimaki, Veijo,Ihee, Hyotcherl,Wulff, Michael International Union of Crystallography 2010 Acta crystallographica. Section A, Foundations of Vol.66 No.2

<P>A time-resolved X-ray solution scattering study of bromine molecules in CCl4is presented as an example of how to track atomic motions in a simple chemical reaction. The structures of the photoproducts are tracked during the recombination process, geminate and non-geminate, from 100 ps to 10 µs after dissociation. The relaxation of hot Br2<SUP>*</SUP>molecules heats the solvent. At early times, from 0.1 to 10 ns, an adiabatic temperature rise is observed, which leads to a pressure gradient that forces the sample to expand. The expansion starts after about 10 ns with the laser beam sizes used here. When thermal artefacts are removed by suitable scaling of the transient solvent response, the excited-state solute structures can be obtained with high fidelity. The analysis shows that 30% of Br2<SUP>*</SUP>molecules recombine directly along the<I>X</I>potential, 60% are trapped in the<I>A</I>/<I>A</I>′ state with a lifetime of 5.5 ns, and 10% recombine non-geminately<I>via</I>diffusive motion in about 25 ns. The Br-Br distance distribution in the<I>A</I>/<I>A</I>′ state peaks at 3.0 Å.</P>

Filming the Birth of Molecules and Accompanying Solvent Rearrangement

Lee, Jae Hyuk,Wulff, Michael,Bratos, Savo,Petersen, Jakob,Guerin, Laurent,Leicknam, Jean-Claude,Cammarata, Marco,Kong, Qingyu,Kim, Jeongho,Møller, Klaus B.,Ihee, Hyotcherl American Chemical Society 2013 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.135 No.8

<P>Molecules are often born with high energy and large-amplitude vibrations. In solution, a newly formed molecule cools down by transferring energy to the surrounding solvent molecules. The progression of the molecular and solute–solvent cage structure during this fundamental process has been elusive, and spectroscopic data generally do not provide such structural information. Here, we use picosecond X-ray liquidography (solution scattering) to visualize time-dependent structural changes associated with the vibrational relaxation of I<SUB>2</SUB> molecules in two different solvents, CCl<SUB>4</SUB> and cyclohexane. The birth and vibrational relaxation of I<SUB>2</SUB> molecules and the associated rearrangement of solvent molecules are mapped out in the form of a temporally varying interatomic distance distribution. The I–I distance increases up to ∼4 Å and returns to the equilibrium distance (2.67 Å) in the ground state, and the first solvation cage expands by ∼1.5 Å along the I–I axis and then shrinks back accompanying the structural change of the I<SUB>2</SUB> molecule.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/2013/jacsat.2013.135.issue-8/ja312513w/production/images/medium/ja-2012-12513w_0007.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ja312513w'>ACS Electronic Supporting Info</A></P>