Chapter 18 THz Investigations of Condensed Phase Biomolecular Systems

Zhang, Ye; Siegrist, K.; Douglas, Kevin O.; Gregurick, Susan K.; Plusquellic, David F.

doi:10.1016/s0091-679x(08)00818-2

Cited by 8 publications

(9 citation statements)

References 38 publications

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“…Due to possible contributions from d ifferent modes occurring at close frequencies, this estimate gives us the upper limit of damping factor , and the lowest limit fo r the time scale of low energy vibrational motions in the sub-THz as ~ 70 ps. Our estimate for a damping coefficient is of the same order as  = 1cm -1 found in [3][4][5][6] at higher frequencies (~1 THz) in experiments based on photomixing technology. In our MD simulat ions, the damping factor was taken as a parameter, and comparison between experimental and calculated spectra was used to adjust its value.…”

Section: Simulation and Discussionsupporting

confidence: 77%

“…Spectral resolution of 0.25-0.3 cm -1 allo ws us to observe spectra rich in resonance features with the spectral lines width of 0.5-1 cm -1 . These spectral line widths are of the same order as those observed in the experiments with high resolution photomixing spectroscopy at higher frequencies (~1THz) [4][5][6]. Test measurements indicate about 80% polarization of the radiation with electric field vector oriented in the vertical direction in Bruker spectrometer.…”

Section: Measurements Of Transmission Spectrasupporting

confidence: 74%

“…The very far in frared (IR) range of absorption reveals these low-energy vib rations, andtheore tical studies predicted mult iple resonances in absorption (or trans mission) spectra of b iological molecu les in the THz frequency (0.1-10 THz ) or millimeter-wavelength (3-300cm − 1) range [2]. Organic solid systems and relatively small bio mo lecules like protein frag ments have beensuccessfully characterized in this range to demonstrate sharp spectral features determined by their individual symmetries and structures [3][4][5][6].…”

Section: Introductionmentioning

confidence: 99%

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Sub-THz Vibrational Spectroscopy of Bacterial Cells and Molecular Components

Globus¹,

Dorofeeva²,

Sizov³

et al. 2012

AJBE

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In this work, sub-terahertz (THz) spectroscopy is applied to characterize lyophilized and in vitro cultured bacterial cells of non-pathogenic species of Escherichia coli (E. coli) and Bacillus subtilis (BG), spores of BG and DNA fro m E. coli. One of the goals of this research is to demonstrate that Fourier Transform (FT) spectroscopy in the frequency region of 10-25 cm -1 is sensitive enough to reveal characteristic spectral features fro m bio-cells and spores in different environment, to verify the d ifferences between species, and to show the response of spores to vacuum and response of cultured cells to heat. The experimental technique was significantly improved for sensitivity and reliab ility. Observed spectra taken with a spectral resolution of 0.25 cm -1 using FT spectrometer with a detector operating at 1.7 K are rich in well resolved features having spectral widths of ~0.5-1 cm -1 . The reproducibility of experimental results was verified and confirmed. Measured spectra from E. coli DNA and from the entire cell have many similarit ies, thus demonstrating that the cellu lar co mponents might contribute to the v ibrational spectrum of the cell. The results of this work confirm that observed spectroscopic features are caused by fundamental physical mechanism of interaction between THz rad iation and biological macro-mo lecules. Particu larly, the analysis of results indicates that the spectroscopic signatures of microorganis ms originate fro m the co mbination of low frequency vibrational modes or group of modes at close frequencies (vibrational bands) within mo lecular co mponents of bacterial cells/spores, with the significant contribution from the DNA. The significance of this study is justified by necessity for a fast and effective, label free and reagent free optical technology to protect against environmental and other biological threats, as well as for general medical research. The obtained results show that THz v ibrational spectroscopy promises to add quantitative genetic information to the characteristic signatures of biological objects, increasing the detection accuracy and selectivity when appropriate spectral resolution is used.

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Section: Simulation and Discussionsupporting

confidence: 77%

Section: Measurements Of Transmission Spectrasupporting

confidence: 74%

Section: Introductionmentioning

confidence: 99%

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Sub-THz Vibrational Spectroscopy of Bacterial Cells and Molecular Components

Globus¹,

Dorofeeva²,

Sizov³

et al. 2012

AJBE

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“…Thus, the lowest limit for the timescale of vibrational motions corresponding to the observed spectral features in the sub-THz range is estimated as τ=1/(γc)∼ 70 ps, where c is the velocity of light. This estimated damping coefficient of 0.5 cm −1 is of the same order as γ= 1 cm −1 , as found in [15][16][17] at higher frequencies (∼1 THz) in experiments based on photomixing technology for highresolution spectroscopy in biosystems.…”

Section: Introductionsupporting

confidence: 77%

Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli

et al. 2011

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Sub-terahertz (THz) vibrational modes of the protein thioredoxin in a water environment were simulated using molecular dynamics (MD) in order to find the conditions needed for simulation convergence, improve the correlation between experimental and simulated absorption frequencies, and ultimately enhance the predictive capabilities of computational modeling. Thioredoxin from E. coli was used as a model molecule for protocol development and to optimize the simulation parameters. The empirically parameterized software packages Amber 8 and 10 were used in this work. Using atomic trajectories from the constant energy and volume MD simulations, thioredoxin's sub-THz vibrational spectra and absorption coefficients were calculated in a quasi-harmonic approximation. An optimal production run length ~100 ps was found, in agreement with experimental data on thioredoxin relaxation dynamics. At the same time, a new procedure was developed for averaging correlation matrices of atomic coordinates in MD simulations. In particular, the open source package ptraj was edited to improve a matrix-analyzing function. Averaging only six matrices gave much more consistent results, with absorption peak intensities exceeding those from the individual spectra and a rather good correlation between simulated vibrational frequencies and experimental data.

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“…These results are also in general agreement with analysis of more broad vibrational features observed at higher frequencies using different experimental technologies, mostly on relatively smaller molecules in crystalline form. Organic solid systems and relatively small bio-molecules like protein fragments have been successfully characterized in this range to demonstrate sharp spectral features determined by their individual symmetries and structures [16][17][18][19].…”

Section: Terahertz Vibratuonal Spectroscopy Of Biological Cells and Cmentioning

confidence: 99%

Teraherz vibrational spectroscopy of <i>E. coli</i> and molecular constituents: Computational modeling and experiment

Globus

Sizov

Gelmont

2013

ABB

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In this paper we present the results of our research of E. coli cells and cellular components, DNA and protein thioredoxin, using highly resolved sub-Terahertz (THz) vibrational spectroscopy. In this combined research, the results from experimental spectroscopy are analyzed via molecular dynamics (MD) simulation of vibrational modes and absorption spectra from E. coli cells and constituents in the sub-THz range. Simplified models of DNA macromolecules with a short sequencing have been constructed for several E. coli strains with the goal to predict their absorption spectra. The similarity between spectral characteristics of E. coli cells and cellular components observed in experiments helps us to better understand the mechanism of material interaction with THz radiation and to add genetic information to the characteristic signatures from biological objects. Modeling results supported by experimental characterization using a spectroscopic sensor prototype developed and built by Vibratess confirm that an optical, label and reagent free technique can be used to examine, detect, and identify bacterial cells with high accuracy and selectivity to the level of strains.

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Chapter 18 THz Investigations of Condensed Phase Biomolecular Systems

Cited by 8 publications

References 38 publications

Sub-THz Vibrational Spectroscopy of Bacterial Cells and Molecular Components

Sub-THz Vibrational Spectroscopy of Bacterial Cells and Molecular Components

Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli

Teraherz vibrational spectroscopy of <i>E. coli</i> and molecular constituents: Computational modeling and experiment

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Chapter 18 THz Investigations of Condensed Phase Biomolecular Systems

Cited by 8 publications

References 38 publications

Sub-THz Vibrational Spectroscopy of Bacterial Cells and Molecular Components

Sub-THz Vibrational Spectroscopy of Bacterial Cells and Molecular Components

Molecular dynamics modeling of the sub-THz vibrational absorption of thioredoxin from E. coli

Teraherz vibrational spectroscopy of &lt;i&gt;E. coli&lt;/i&gt; and molecular constituents: Computational modeling and experiment

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Teraherz vibrational spectroscopy of <i>E. coli</i> and molecular constituents: Computational modeling and experiment