01739nas a2200205 4500008004500000020001400045245008900059210006900148260000800217300001400225490000800239520112900247653001501376100002101391700001701412700001901429700001601448700002001464856004901484 2020 Engldsh a0006-349500aLong Range Correlated Motions of TIM and their Possible Influence on Enzyme Function0 aLong Range Correlated Motions of TIM and their Possible Influenc cFeb a207A-207A0 v1183 a
The alpha-beta barrel structure of triosephosphate isomerase (TIM) is possibly the most common among enzymes. In the case of TIM, structural dynamics are known to be essential to function. In particular the stabilization of the binding pocket by a phosphodianion “handle” of the substrate and the closing of catalytic site loops 6 and 7 over the substrate. Loop 6 moves by as much as 7 Angstroms with binding. Recently a mutant survey for human TIM (hsTIM) found kcat can change significantly for a single mutation distant from the catalytic site. Crystallographic measurements find no structural change with the mutation, suggesting a dynamical mechanism for the allosteric effect. Here we use Stationary Sample Anisotropic Terahertz Microscopy (SSATM) to measure the long-range intramolecular vibrations and determine if specific vibrations couple the allosteric and catalytic sites. SSATM isolated protein long-range structural vibrations based on the dominant displacement direction [1-4]. We examine if specific vibrational bands are associate with loop 6 and loop 7 flexibility.
10aBiophysics1 aMcKinney, J., A.1 aDeng, Y., T.1 aGeorge, D., K.1 aRichard, J.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/25202692nas a2200265 4500008004500000020001400045245010200059210006900161260000800230300001400238490000700252520189600259653001402155653002102169653002302190653002802213653003102241653001702272653001002289653002202299100001702321700001902338700002002357856004902377 2020 Engldsh a1549-959600aPersistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis0 aPersistent Protein Motions in a Rugged Energy Landscape Revealed cDec a6419-64260 v603 aProteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 mu s of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.
10aChemistry10aComputer Science10amolecular-dynamics10aPharmacology & Pharmacy10aphotoactive yellow protein10aspectroscopy10astate10avibrational-modes1 aRomo, T., D.1 aGrossfield, A.1 aMarkelz, A., G. uhttps://markelz.physics.buffalo.edu/node/24100492nas a2200145 4500008004100000245008500041210006900126260001200195100001300207700001700220700001300237700001900250700002000269856005700289 2019 eng d00aProtein Intramolecular Motions with Deuteration and Inhibitor Binding Dependence0 aProtein Intramolecular Motions with Deuteration and Inhibitor Bi c03/20191 aDeng, Y.1 aMcKinney, J.1 aRomo, T.1 aGrossfield, A.1 aMarkelz, A., G. uhttps://meetings.aps.org/Meeting/MAR19/Session/R63.302599nas a2200205 4500008004500000020001400045245005800059210005800117260000800175300001400183490000800197520204200205653001502247100001702262700001702279700001302296700001902309700001602328856004902344 2019 Engldsh a0006-349500aSpectral Assignment of Lysozyme Collective Vibrations0 aSpectral Assignment of Lysozyme Collective Vibrations cFeb a564A-564A0 v1163 aScience and technologies based on terahertz frequency electromagnetic radiation (100 GHz-30 THz) have developed rapidly over the last 30 years. For most of the 20th Century, terahertz radiation, then referred to as sub-millimeter wave or far-infrared radiation, was mainly utilized by astronomers and some spectroscopists. Following the development of laser based terahertz time-domain spectroscopy in the 1980s and 1990s the field of THz science and technology expanded rapidly, to the extent that it now touches many areas from fundamental science to 'real world' applications. For example THz radiation is being used to optimize materials for new solar cells, and may also be a key technology for the next generation of airport security scanners. While the field was emerging it was possible to keep track of all new developments, however now the field has grown so much that it is increasingly difficult to follow the diverse range of new discoveries and applications that are appearing. At this point in time, when the field of THz science and technology is moving from an emerging to a more established and interdisciplinary field, it is apt to present a roadmap to help identify the breadth and future directions of the field. The aim of this roadmap is to present a snapshot of the present state of THz science and technology in 2017, and provide an opinion on the challenges and opportunities that the future holds. To be able to achieve this aim, we have invited a group of international experts to write 18 sections that cover most of the key areas of THz science and technology. We hope that The 2017 Roadmap on THz science and technology will prove to be a useful resource by providing a wide ranging introduction to the capabilities of THz radiation for those outside or just entering the field as well as providing perspective and breadth for those who are well established. We also feel that this review should serve as a useful guide for government and funding agencies.
10aex-vivo10ageneration10ametal wave-guides10anear-field10aperformance10aphotoconductive emitters10aPhysics10aquantum-cascade lasers10aradiation10asemiconductors10aTerahertz10athz10atime-domain spectroscopy1 aDhillon, S., S.1 aVitiello, M., S.1 aLinfield, E., H.1 aDavies, A., G.1 aHoffmann, M., C.1 aBooske, J.1 aPaoloni, C.1 aGensch, M.1 aWeightman, P.1 aWilliams, G., P.1 aCastro-Camus, E.1 aCumming, D., R. S.1 aSimoens, F.1 aEscorcia-Carranza, I.1 aGrant, J.1 aLucyszyn, S.1 aKuwata-Gonokami, M.1 aKonishi, K.1 aKoch, M.1 aSchmuttenmaer, C., A.1 aCocker, T., L.1 aHuber, R.1 aMarkelz, A., G.1 aTaylor, Z., D.1 aWallace, V., P.1 aZeitler, J., A.1 aSibik, J.1 aKorter, T., M.1 aEllison, B.1 aRea, S.1 aGoldsmith, P.1 aCooper, K., B.1 aAppleby, R.1 aPardo, D.1 aHuggard, P., G.1 aKrozer, V.1 aShams, H.1 aFice, M.1 aRenaud, C.1 aSeeds, A.1 aStohr, A.1 aNaftaly, M.1 aRidler, N.1 aClarke, R.1 aCunningham, J., E.1 aJohnston, M., B. uhttps://markelz.physics.buffalo.edu/node/22401243nas a2200313 4500008004500000020002200045245007500067210006900142260004900211490000900260520038500269653001200654653001300666653001400679653001100693653001300704653001300717653001500730653001700745653001400762653000800776100001400784700001500798700001500813700002000828700001600848700001600864856004900880 2009 Engldsh a978-0-8194-7687-600aThe role of the protein surface on the local biological water dynamics0 arole of the protein surface on the local biological water dynami aBellinghambSpie-Int Soc Optical Engineering0 v73973 aProtein function is reliant on structural flexibility and this flexibility is slaved to the surrounding solvent. Here we discuss how the exposed surface of the protein influences the solvent dynamics and thereby influences the protein's own structural dynamics. We discuss measurements of the THz absorption of water in the presence of hydrophilic and hydrophobic surfaces.
10aalanine10adynamics10ahydration10alysine10alysozyme10aproteins10arelaxation10aspectroscopy10aTerahertz10athz1 aLiang, W.1 aHe, Y., F.1 aGeorge, D.1 aMarkelz, A., G.1 aRazeghi, M.1 aMohseni, H. uhttps://markelz.physics.buffalo.edu/node/23201467nas a2200349 4500008004500000020001400045245004900059210004900108260000800157300000600165490000700171520058300178653001300761653001200774653002900786653001200815653001700827653001400844653002300858653001700881653001400898100001700912700001800929700001500947700001800962700001800980700001600998700001701014700002001031700001701051856004901068 2008 Engldsh a0003-695100aTerahertz response of quantum point contacts0 aTerahertz response of quantum point contacts cJun a30 v923 aWe measure a clear terahertz response in the low-temperature conductance of a quantum point contact at 1.4 and 2.5 THz. We show that this photoresponse does not arise from a heating effect, but that it is instead excellently described by a classical model of terahertz-induced gate-voltage rectification. This effect is distinct from the rectification mechanisms that have been studied previously, being determined by the phase-dependent interference of the source drain and gate voltage modulations induced by the terahertz field. (C) 2008 American Institute of Physics.
10adetector10adevices10afield-effect transistors10aPhysics10aplasma-waves10aradiation10aresonant detection10asubterahertz10atransport1 aSong, J., W.1 aKabir, N., A.1 aKawano, Y.1 aIshibashi, K.1 aAizin, G., R.1 aMourokh, L.1 aReno, J., L.1 aMarkelz, A., G.1 aBird, J., P. uhttps://markelz.physics.buffalo.edu/node/24301575nas a2200337 4500008004500000020001400045245011100059210006900170260000800239300000600247490000700253520062400260653002900884653002200913653001200935653001700947653001400964653002300978653001701001100001801018700001301036700001701049700001701066700002001083700001701103700001701120700001601137700001801153700001701171856004901188 2006 Engldsh a0003-695100aTerahertz transmission characteristics of high-mobility GaAs and InAs two-dimensional-electron-gas systems0 aTerahertz transmission characteristics of highmobility GaAs and cSep a30 v893 aFrequency-dependent complex conductivity of high-mobility GaAs and InAs two-dimensional-electron-gas (2DEG) systems is studied by terahertz time domain spectroscopy. Determining the momentum relaxation time from a Drude model, the authors find a lower value than that from dc measurements, particularly at high frequencies/low temperatures. These deviations are consistent with the ratio tau(t)/tau(q,) where tau(q) is the full scattering time. This suggests that small-angle scattering leads to weaker heating of 2DEGs at low temperatures than expected from dc mobilit9y. (c) 2006 American Institute of Physics.
10afield-effect transistors10aphotoconductivity10aPhysics10aplasma-waves10aradiation10aresonant detection10asubterahertz1 aKabir, N., A.1 aYoon, Y.1 aKnab, J., R.1 aChen, J., Y.1 aMarkelz, A., G.1 aReno, J., L.1 aSadofyev, Y.1 aJohnson, S.1 aZhang, Y., H.1 aBird, J., P. uhttps://markelz.physics.buffalo.edu/node/22901306nas a2200325 4500008004100000020001400041245006500055210006500120260001600185300001400201490000700215520044400222653001900666653001600685653001900701653001200720653002300732653001400755100001500769700001500784700001300799700001200812700001100824700001300835700001700848700001200865700001400877700001700891856007200908 2003 eng d a1386-947700aDirect measurements of optical phonons in SrTiO3 nanosystems0 aDirect measurements of optical phonons in SrTiO3 nanosystems c2003/07/01/ a236 - 2390 v193 aWe use terahertz time domain spectroscopy to examine finite size effects on the optical phonon modes in SrTiO3 thin films. In temperature-dependent measurements we find a near absence of mode softening in the TO1 phonon frequency. Furthermore we see an increase in the soft mode frequency with reduced thickness. Both of these results correlate well with the reduced dielectric response observed for nanoscale ferroelectric systems.
10aFerroelectrics10aFinite size10aMode softening10aphonons10aStrontium titanate10aTerahertz1 aWolpert, D1 aKorolev, K1 aSachs, S1 aKnab, J1 aCox, W1 aCerne, J1 aMarkelz, A.G1 aZhao, T1 aRamesh, R1 aMoeckly, B.H uhttps://www.sciencedirect.com/science/article/pii/S138694770300305901941nas a2200373 4500008004100000020001500041245008000056210006900136260003100205300001000236490000600246520087600252653002801128653004401156653002101200653001901221653001901240653002901259653002401288653001801312653001701330653002201347653001201369653001201381653002001393100001601413700001201429700001401441700001601455700001301471700001501484700001901499856004901518 2003 eng d a097284220900aFinite size effects in ferroelectric nanosystems: Absence of mode softening0 aFinite size effects in ferroelectric nanosystems Absence of mode aSan Francisco, CAc02/2003 a76-810 v23 aWe present measurements of the mode softening behavior for PbZr 0.5Ti0.5O3 (PZT(50)) thin films using terahertz time domain spectroscopy (TTDS). The films were grown using pulsed laser deposition (PLD) techniques on silicon substrates to study how reduced size affects the mode softening behavior. At room temperature two modes are observed at 1.1 THz (37 cm-1) and at 2.3 THz (77 cm-1). As the temperature is increased toward Tc we do not see strong mode softening, but rather a spectral weight transfer from the high frequency mode to the low frequency mode. This absence of mode softening is more dramatic than that reported by other investigators[1]. We will discuss the possible sources for this discrepancy. These results suggest a change in lattice dynamics for nanoscale ferroelectric films that may be highly dependent on the sample preparation technique.
10aFerroelectric materials10aFourier Transform Infrared Spectroscopy10aFrequency ranges10aLead compounds10aMode softening10ananostructured materials10aNatural frequencies10aOptical modes10aPermittivity10aphase transitions10aphonons10aRouters10aThermal effects1 aWolpert, D.1 aCox, W.1 aCerne, J.1 aMarkelz, A.1 aZhao, T.1 aRamesh, R.1 aM., Romanowicz uhttps://markelz.physics.buffalo.edu/node/27501285nas a2200241 4500008004500000020001400045245010000059210006900159260000800228300001000236490000800246520061300254653001000867653001400877653001000891653001000901653001200911653001300923100002000936700001700956700002100973856004900994 2000 Engldsh a0009-261400aPulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz0 aPulsed terahertz spectroscopy of DNA bovine serum albumin and co cMar a42-480 v3203 aWe report the first use of pulsed terahertz spectroscopy to examine low-frequency collective vibrational modes of biomolecules. Broadband absorption increasing with frequency was observed for lyophilized powder samples of calf thymus DNA, bovine serum albumin and collagen in the 0.06-2.00 THz (2-67 cm(-1)) frequency range, suggesting that a large number of the low-frequency collective modes for these systems are IR active. Transmission measurements at room temperature showed increasing FIR absorption with hydration and denaturing. (C) 2000 published by Elsevier Science B.V. All rights reserved.
10ab-dna10aChemistry10afilms10amodes10aPhysics10aproteins1 aMarkelz, A., G.1 aRoitberg, A.1 aHeilweil, E., J. uhttps://markelz.physics.buffalo.edu/node/27100500nas a2200169 4500008004100000245003800041210003800079260001300117100002100130700002000151700001600171700002100187700001800208700001700226700002000243856006700263 1995 eng d00aTerahertz grid frequency doublers0 aTerahertz grid frequency doublers bCiteseer1 aChiao, Jung-Chih1 aMarkelz, Andrea1 aLi, Yongjun1 aHacker, Jonathan1 aCrowe, Thomas1 aAllen, James1 aRutledge, David uhttps://www.nrao.edu/meetings/isstt/papers/1995/1995199206.pdf01594nas a2200337 4500008004100000020001400041245009400055210006900149260000800218300001200226490000900238520066100247100001800908700001400926700001800940700001800958700001900976700002100995700001701016700002001033700001501053700001801068700002001086700002001106700002001126700002001146700001301166700001201179700001601191856004901207 1994 eng d a0022-231300aPROBING TERAHERTZ DYNAMICS IN SEMICONDUCTOR NANOSTRUCTURES WITH UCSB FREE-ELECTRON LASERS0 aPROBING TERAHERTZ DYNAMICS IN SEMICONDUCTOR NANOSTRUCTURES WITH cApr a250-2550 v60-13 aThe UCSB free-electron lasers provide kilowatts of continuously tunable radiation from 120 GHz to 4.8 THz. They have the most impact on terahertz science and technology that require a tunable, high power source to explore non-linear dynamics or that sacrifice incident power to recover the linear response of systems with very small cross-section. We describe three experiments that demonstrate the utility of these lasers in experiments on the terahertz dynamics of semiconductor nanostructures: (i) terahertz dynamics of resonant tunneling diodes, (ii) saturation spectroscopy of quantum wells and (iii) photon-assisted tunneling in superlattices.
1 aAllen, S., J.1 aCraig, K.1 aFelix, C., L.1 aGuimaraes, P.1 aHeyman, J., N.1 aKaminski, J., P.1 aKeay, B., J.1 aMarkelz, A., G.1 aRamian, G.1 aScott, J., S.1 aSherwin, M., S.1 aCampman, K., L.1 aHopkins, P., F.1 aGossard, A., C.1 aChow, D.1 aLui, M.1 aLiu, T., Y. uhttps://markelz.physics.buffalo.edu/node/257