Browsing by Subject "SPECTROSCOPY"

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  • Huotari, S.; Sahle, Ch J.; Henriquet, Ch; Al-Zein, A.; Martel, K.; Simonelli, L.; Verbeni, R.; Gonzalez, H.; Lagier, M. -C.; Ponchut, C.; Sala, M. Moretti; Krisch, M.; Monaco, G. (2017)
    An end-station for X-ray Raman scattering spectroscopy at beamline ID20 of the European Synchrotron Radiation Facility is described. This end-station is dedicated to the study of shallow core electronic excitations using non-resonant inelastic X-ray scattering. The spectrometer has 72 spherically bent analyzer crystals arranged in six modular groups of 12 analyzer crystals each for a combined maximum flexibility and large solid angle of detection. Each of the six analyzer modules houses one pixelated area detector allowing for X-ray Raman scattering based imaging and efficient separation of the desired signal from the sample and spurious scattering from the often used complicated sample environments. This new end-station provides an unprecedented instrument for X-ray Raman scattering, which is a spectroscopic tool of great interest for the study of low-energy X-ray absorption spectra in materials under insitu conditions, such as inoperando batteries and fuel cells, insitu catalytic reactions, and extreme pressure and temperature conditions.
  • Hänninen, Vesa; Murdachaew, Garold; Nathanson, Gilbert M.; Gerber, R. Benny; Halonen, Lauri (2018)
    Ab initio molecular dynamics simulations of formic acid (FA) dimer colliding with liquid water at 300 K have been performed using density functional theory. The two energetically lowest FA dimer isomers were collided with a water slab at thermal and high kinetic energies up to 68k(B)T. Our simulations agree with recent experimental observations of nearly a complete uptake of gas-phase FA dimer: the calculated average kinetic energy of the dimers immediately after collision is 5 +/- 4% of the incoming kinetic energy, which compares well with the experimental value of 10%. Simulations support the experimental observation of no delayed desorption of FA dimers following initial adsorption. Our analysis shows that the FA dimer forms hydrogen bonds with surface water molecules, where the hydrogen bond order depends on the dimer structure, such that the most stable isomer possesses fewer FA-water hydrogen bonds than the higher energy isomer. Nevertheless, even the most stable isomer can attach to the surface through one hydrogen bond despite its reduced hydrophilicity. Our simulations further show that the probability of FA dimer dissociation is increased by high collision energies, the dimer undergoes isomerization from the higher energy to the lowest energy isomer, and concerted double-proton transfer occurs between the FA monomers. Interestingly, proton transfer appears to be driven by the release of energy arising from such isomerization, which stimulates those internal vibrational degrees of freedom that overcome the barrier of a proton transfer.
  • Martikainen, Julia; Penttilä, Antti; Gritsevich, M.; Videen, Gorden; Muinonen, Karri Olavi (2019)
    We present a new physics-based approach to model the absolute reflectance spectra of asteroid (4) Vesta. The spectral models are derived by utilizing a ray-optics code that simulates light scattering by particles large compared to the wavelength of the incident light. In the light of the spectral data obtained by the Dawn spacecraft, we use howardite powder to model Vesta's surface regolith and its particle size distribution for 10-200 mu m sized particles. Our results show that the modelled spectrum mimics well the observations. The best match was found using a power-law particle size distribution with an index 3.2. This suggests that Vesta's regolith is dominated by howardite particles
  • Khakalo, Alexey; Tanaka, Atsushi; Korpela, Antti; Hauru, Lauri K. J.; Orelma, Hannes (2019)
    Synthetic structural materials of high mechanical performance are typically either of large weight (for example, steels, and alloys) or involve complex manufacturing processes and thus have high cost or cause adverse environmental impact (for example, polymer-based and biomimetic composites). In this perspective, low-cost, abundant and nature-based materials, such as wood, represent particular interest provided they fulfill the requirements for advanced engineering structures and applications, especially when manufactured totally additive-free. Here, we report on a novel all-wood material concept based on delignification, partial surface dissolution using ionic liquid (IL) followed by densification resulting in a high-performance material. A delignification process using sodium chlorite in acetate buffer solution was applied to controllably delignify the entire bulk wooden material while retaining the highly beneficial structural directionality of wood. In a subsequent step, obtained delignified porous wood template was infiltrated with an IL 1-ethyl-3-methylimidazolium acetate, [EMIM]OAc and heat activated at 95 degrees C to partially dissolve the fiber surface. Afterward, treated wood was washed with water to remove IL and hot-pressed to gain a very compact cellulosic material with fused fibers while retaining unidirectional fiber orientation. The obtained cellulose materials were structurally, chemically, and mechanically characterized revealing superior tensile properties compared to native wood. Furthermore, suggested approach allows almost 8-fold tensile strength improvement in the direction perpendicular to fiber orientation, which is otherwise very challenging to achieve.
  • Zellweger, Christoph; Emmenegger, Lukas; Firdaus, Mohd; Hatakka, Juha; Heimann, Martin; Kozlova, Elena; Spain, T. Gerard; Steinbacher, Martin; van der Schoot, Marcel V.; Buchmann, Brigitte (2016)
    Until recently, atmospheric carbon dioxide (CO2) and methane (CH4) measurements were made almost exclusively using nondispersive infrared (NDIR) absorption and gas chromatography with flame ionisation detection (GC/FID) techniques, respectively. Recently, commercially available instruments based on spectroscopic techniques such as cavity ring-down spectroscopy (CRDS), off-axis integrated cavity output spectroscopy (OA-ICOS) and Fourier transform infrared (FTIR) spectroscopy have become more widely available and affordable. This resulted in a widespread use of these techniques at many measurement stations. This paper is focused on the comparison between a CRDS "travelling instrument" that has been used during performance audits within the Global Atmosphere Watch (GAW) programme of the World Meteorological Organization (WMO) with instruments incorporating other, more traditional techniques for measuring CO2 and CH4 (NDIR and GC/FID). We demonstrate that CRDS instruments and likely other spectroscopic techniques are suitable for WMO/GAW stations and allow a smooth continuation of historic CO2 and CH4 time series. Moreover, the analysis of the audit results indicates that the spectroscopic techniques have a number of advantages over the traditional methods which will lead to the improved accuracy of atmospheric CO2 and CH4 measurements.
  • Holmstrom, E.; Kotakoski, J.; Lechner, L.; Kaiser, U.; Nordlund, K. (2012)
  • IDS Collaboration; Piersa, M.; Rahkila, P. (2019)
    Excited states in Sn-133 were investigated through the beta decay of In-133 at the ISOLDE facility. The ISOLDE Resonance Ionization Laser Ion Source (RILIS) provided isomer-selective ionization for In-133, allowing us to study separately, and in detail, the beta-decay branch of In-133 J(pi)= (9/2(+)) ground state and its J(pi) = (1/2(-)) isomer.Thanks to the large spin difference of the two beta-decaying states of In-133, it is possible to investigate separately the lower and higher spin states in the daughter, Sn-133, and thus to probe independently different single-particle and single-hole levels. We report here new gamma transitions observed in the decay of In-133, including those assigned to the deexcitation of the neutron-unbound states.
  • Bjorkman, Mikko P.; Pitkala, Kaisu H.; Jyvakorpi, Satu; Strandberg, Timo E.; Tilvis, Reijo S. (2019)
    Objectives: To assess the prognostic significance of various characteristics and measurements of sarcopenia and physical functioning on all-cause mortality among home-dwelling older people with or at-risk of sarcopenia. Design: Cross-sectional and longitudinal analyses. Setting: Porvoo sarcopenia trial in open care. Participants: Community-dwelling people aged 75 and older (N = 428, of which 182 were re-examined at one year) with four years of follow-up. Measurements: Body mass index (BMI), physical functioning (physical component of the RAND-36) and physical performance tests (Short Physical Performance Battery (SPPB)), hand grip strength, walking speed, Charlson Comorbity Index, bioimpedance-based surrogates for muscle mass: Single Frequency Skeletal Muscle Index (SF-SMI), and Calf Intracellular Resistance Skeletal Muscle Index (CRi-SMI). Date of death was retrieved from central registers. Survival analyses were performed using Life-Table analyses and Cox models. Results: Most test variables (except BMI) were associated with four-year mortality in a dose-dependent fashion. After controlling for age, gender and co-morbidity, physical performance and functioning (both SPPB and RAND36), muscle strength (hand grip strength) and CRi-SMI appeared to be independent mortality risk indicators (p <0.001) whereas SF-SMI was not. When CRi-SMI values were grouped by gender-specific cut-off points, the probability of surviving for four years decreased by 66% among the older people with low CRi-SMI (HR = 0.34, 95%CI 0.15-0.78, p = 0.011). When low CRi-SMI was further controlled for SPPB, the prognostic significance remained significant (HR = 0.55, 95%CI 0.33-0.92, p = 0.021). After controlling for age, gender, comorbidity, and CRi-SMI, the physical component of the RAND-36 (p = 0.007), SPPB (p <0,001) and hand grip strength (p = 0.009) remained significant mortality predictors. Twelve-month changes were similarly associated with allcause mortality during the follow-up period. Conclusion: CRi-SMI, muscle strength, physical performance and physical functioning are each strong independent predictors of all-cause mortality among home-dwelling older people. Compared to these indicators, BMI seemed to be clearly inferior. Of two bioimpedance-based muscle indices, CRi SMI was better predictor of mortality than SF-SMI. In this regard, muscle mass, muscle strength and physical performance are all suitable targets for the prevention of sarcopenia-related over-mortality.
  • Parkkila, Petteri; Elderdfi, Mohamed; Bunker, Alex; Viitala, Tapani (2018)
    Supported lipid bilayers (SLBs) have been used extensively as an effective model of biological membranes, in the context of in vitro biophysics research, and the membranes of liposomes, in the context of the development of nanoscale drug delivery devices. Despite numerous surface-sensitive techniques having been applied to their study, the comprehensive optical characterization of SLBs using surface plasmon resonance (SPR) has not been conducted. In this study, Fresnel multilayer analysis is utilized to effectively calculate layer parameters (thickness and refractive indices) with the aid of dual-wavelength and dispersion coefficient analysis, in which the linear change in the refractive index as a function of wavelength is assumed. Using complementary information from impedance-based quartz crystal microbalance experiments, biophysical properties, for example, area-per-lipid-molecule and the quantity of lipid-associated water molecules, are calculated for different lipid types and mixtures, one of which is representative of a raft-forming lipid mixture. It is proposed that the hydration layer beneath the bilayer is, in fact, an integral part of the measured optical signal. Also, the traditional Jung model analysis and the ratio of SPR responses are investigated in terms of assessing the structure of the lipid layer that is formed.
  • Bowles, N. E.; Snodgrass, C.; Gibbings, A.; Sanchez, J. P.; Arnold, J. A.; Eccleston, P.; Andert, T.; Probst, A.; Naletto, G.; Vandaele, A. C.; de Leon, J.; Nathues, A.; Thomas, I. R.; Thomas, N.; Jorda, L.; Da Deppo, V.; Haack, H.; Green, S. F.; Carry, B.; Hanna, K. L. Donaldson; Jorgensen, J. Leif; Kereszturi, A.; DeMeo, F. E.; Patel, M. R.; Davies, J. K.; Clarke, F.; Kinch, K.; Guilbert-Lepoutre, A.; Agarwal, J.; Rivkin, A. S.; Pravec, P.; Fornasier, S.; Granvik, M.; Jones, R. H.; Murdoch, N.; Joy, K. H.; Pascale, E.; Tecza, M.; Barnes, J. M.; Licandro, J.; Greenhagen, B. T.; Calcutt, S. B.; Marriner, C. M.; Warren, T.; Tosh, I. (2018)
    CASTAway is a mission concept to explore our Solar System's main asteroid belt. Asteroids and comets provide a window into the formation and evolution of our Solar System and the composition of these objects can be inferred from space-based remote sensing using spectroscopic techniques. Variations in composition across the asteroid populations provide a tracer for the dynamical evolution of the Solar System. The mission combines a long-range (point source) telescopic survey of over 10,000 objects, targeted close encounters with 10-20 asteroids and serendipitous searches to constrain the distribution of smaller (e.g. 10 m) size objects into a single concept. With a carefully targeted trajectory that loops through the asteroid belt, CASTAway would provide a comprehensive survey of the main belt at multiple scales. The scientific payload comprises a 50 cm diameter telescope that includes an integrated low-resolution (R = 30-100) spectrometer and visible context imager, a thermal (e.g. 6-16 mu m) imager for use during the flybys, and modified star tracker cameras to detect small (similar to 10 m) asteroids. The CASTAway spacecraft and payload have high levels of technology readiness and are designed to fit within the programmatic and cost caps for a European Space Agency medium class mission, while delivering a significant increase in knowledge of our Solar System. (C) 2017 COSPAR. Published by Elsevier Ltd. All rights reserved.
  • Saarinen, Jukka Kalle Samuel; Gütter, Friederike; Lindman, Mervi M; Agopov, Mikael; Fraser-Miller, Sara J.; Scherließ, Regina; Jokitalo, Eija; Almeida Santos, Helder; Peltonen, Leena; Isomäki, Antti; Strachan, Clare J. (2019)
    A wide variety of nanoparticles are playing an increasingly important role in drug delivery. Label-free imaging techniques are especially desirable to follow the cellular uptake and intracellular fate of nanoparticles. The combined correlative use of different techniques, each with unique advantages, facilitates more detailed investigation about such interactions. The synergistic use of correlative coherent anti-Stokes Raman scattering and electron microscopy (C-CARS-EM) imaging offers label-free, chemically-specific, and (sub)-nanometer spatial resolution for studying nanoparticle uptake into cells as demonstrated in the current study. Coherent anti-Stokes Raman scattering (CARS) microscopy offers chemically-specific (sub)micron spatial resolution imaging without fluorescent labels while transmission electron microscopy (TEM) offers (sub)-nanometer scale spatial resolution and thus visualization of precise nanoparticle localization at the sub-cellular level. This proof-of-concept imaging platform with unlabeled drug nanocrystals and macrophage cells revealed good colocalization between the CARS signal and electron dense nanocrystals in TEM images. The correlative TEM images revealed subcellular localization of nanocrystals inside membrane bound vesicles, showing multivesicular body (MVB)-like morphology typical for late endosomes (LEs), endolysosomes, and phagolysosomes. C-CARS-EM imaging has much potential to study the interactions between a wide range of nanoparticles and cells with high precision and confidence.
  • Lang, Adam R.; Engelberg, Dirk L.; Walther, Clemens; Weiss, Martin; Bosco, Hauke; Jenkins, Alex; Livens, Francis R.; Law, Gareth T. W. (2019)
    Stainless steels can become contaminated with radionuclides at nuclear sites. Their disposal as radioactive waste would be costly. If the nature of steel contamination could be understood, effective decontamination strategies could be designed and implemented during nuclear site decommissioning in an effort to release the steels from regulatory control. Here, batch uptake experiments have been used to understand Sr and Cs (fission product radionuclides) uptake onto AISI Type 304 stainless steel under conditions representative of spent nuclear fuel storage (alkaline ponds) and PUREX nuclear fuel reprocessing (HNO3). Solution (ICP-MS) and surface measurements (GD-OES depth profiling, TOF-SIMS, and XPS) and kinetic modeling of Sr and Cs removal from solution were used to characterize their uptake onto the steel and define the chemical composition and structure of the passive layer formed on the steel surfaces. Under passivating conditions (when the steel was exposed to solutions representative of alkaline ponds and 3 and 6 M HNO3), Sr and Cs were maintained at the steel surface by sorption/selective incorporation into the Cr-rich passive film. In 12 M HNO3, corrosion and severe intergranular attack led to Sr diffusion into the passive layer and steel bulk. In HNO3, Sr and Cs accumulation was also commensurate with corrosion product (Fe and Cr) readsorption, and in the 12 M HNO3 system, XPS documented the presence of Sr and Cs chromates.
  • Rahkila, Jani; Ekholm, Filip S.; Leino, Reko (2018)
    Biomass derived oligo- and polysaccharides are important compounds for various applications, including biomedicine and material science. Their use, however, is often limited by inherent structural inhomogeneity of the starting materials. Here, a method for depolymerization of naturally occurring polysaccharides, including dextran, starch, xylan and galactoglucomannan, into well-defined fragments of narrow polydispersities is described, based on the use of in situ generated Cu-I species under the commonly employed CuAAC reaction conditions. The main strength of the reported method is its high versatility, both in terms of substrate scope and operational simplicity.
  • Lundbom, Jesper; Bierwagen, Alessandra; Bodis, Kalman; Szendroedi, Julia; Kaprio, Jaakko; Rissanen, Aila; Lundbom, Nina; Roden, Michael; Pietilainen, Kirsi H. (2016)
    Background. Obese twins have lower saturated and higher long-chain polyunsaturated fatty acids (FA) in subcutaneous adipose tissue (SAT) compared to their lean monozygotic (MZ) co-twin. Whether this holds for metabolically distinct deep (DSAT) and superficial (SSAT) depots is unknown. Here we use non-invasive magnetic resonance spectroscopy (MRS) to measure the FA unsaturation in body mass index (BMI) discordant MZ twins in DSAT and SSAT and their relationship to ectopic fat content and body fat distribution. The main finding is further confirmed in an independent cohort using standardized measurement times. Methods. MRS and magnetic resonance imaging were used to measure DSAT and SSAT unsaturation and their relationship to intramyocellular lipids (IMCL), hepatocellular lipids (HCL) and the amount of subcutaneous (SAT) and visceral adipose tissue (VAT) in 16 pairs of healthy monozygotic twins (MZ) discordant for BMI. A second independent cohort of 12 healthy volunteers was used to measure DSAT unsaturation and IMCL with standardized measurement time. One volunteer also underwent repeated random measurements of DSAT unsaturation and IMCL. Results. In accordance with biopsy studies SSAT unsaturation was higher in the heavier twins (15.2 +/- 1.0% vs. 14.4 +/- 1.5%, P = 0.024) and associated with SAT volume (R = 0.672, P = 0.001). DSAT unsaturation did not differ between twins (11.4 +/- 0.8 vs. 11.0 +/- 1.0, P = 0.267) and associated inversely with IMCL content (R = -0.462, P = 0.001). The inverse association between DSAT unsaturation and IMCL was also present in the participants of the second cohort (R = -0.641, P = 0.025) and for the repeated sampling at random of one person (R = -0.765, P = 0.027). Conclusions. DSAT and SSAT FA unsaturation shows distinct associations with obesity and IMCL in MZ twins, reflecting compartment-specific metabolic activities. The FA unsaturation in the DSAT depot associates inversely with IMCL content, which raises the possibility of cross talk between the DSAT depot and the rapid turnover IMCL depot. (C) 2016 Elsevier Inc. All rights reserved.
  • Karhu, Juho; Nauta, Janko; Vainio, Markku Mikael; Metsälä, Markus Ilari; Hoekstra, Steven; Halonen, Lauri Olavi (2016)
    A novel mid-infrared/near-infrared double resonant absorption setup for studying infrared-inactive vibrational states is presented. A strong vibrational transition in the mid-infrared region is excited using an idler beam from a singly resonant continuous-wave optical parametric oscillator, to populate an intermediate vibrational state. High output power of the optical parametric oscillator and the strength of the mid-infrared transition result in efficient population transfer to the intermediate state, which allows measuring secondary transitions from this state with a high signal-to-noise ratio. A secondary, near-infrared transition from the intermediate state is probed using cavity ring-down spectroscopy, which provides high sensitivity in this wavelength region. Due to the narrow linewidths of the excitation sources, the rovibrational lines of the secondary transition are measured with sub-Doppler resolution. The setup is used to access a previously unreported symmetric vibrational state of acetylene, nu(1) + nu(2) + nu(3) + nu(1)(4) + nu(-1)(5) in the normal mode notation. Single-photon transitions to this state from the vibrational ground state are forbidden. Ten lines of the newly measured state are observed and fitted with the linear least-squares method to extract the band parameters. The vibrational term value was measured to be at 9775.0018(45) cm(-1), the rotational parameter B was 1.162 222(37) cm(-1), and the quartic centrifugal distortion parameter D was 3.998(62) x 10(-6) cm(-1), where the numbers in the parenthesis are one-standard errors in the least significant digits. Published by AIP Publishing.
  • Luukkonen, Panu K.; Dufour, Sylvie; Lyu, Kun; Zhang, Xian-Man; Hakkarainen, Antti; Lehtimäki, Tiina E.; Cline, Gary W.; Petersen, Kitt Falk; Shulman, Gerald I.; Yki-Järvinen, Hannele (2020)
    Weight loss by ketogenic diet (KD) has gained popularity in management of nonalcoholic fatty liver disease (NAFLD). KD rapidly reverses NAFLD and insulin resistance despite increasing circulating nonesterified fatty acids (NEFA), the main substrate for synthesis of intrahepatic triglycerides (IHTG). To explore the underlying mechanism, we quantified hepatic mitochondrial fluxes and their regulators in humans by using positional isotopomer NMR tracer analysis. Ten overweight/obese subjects received stable isotope infusions of: [D-7]glucose, [C-13(4)]beta-hydroxybutyrate and [3-C-13]lactate before and after a 6-d KD. IHTG was determined by proton magnetic resonance spectroscopy (H-1-MRS). The KD diet decreased IHTG by 31% in the face of a 3% decrease in body weight and decreased hepatic insulin resistance (-58%) despite an increase in NEFA concentrations (+35%). These changes were attributed to increased net hydrolysis of IHTG and partitioning of the resulting fatty acids toward keto-genesis (+232%) due to reductions in serum insulin concentrations (-53%) and hepatic citrate synthase flux (-38%), respectively. The former was attributed to decreased hepatic insulin resistance and the latter to increased hepatic mitochondrial redox state (+167%) and decreased plasma leptin (-45%) and triiodothyronine (-21%) concentrations. These data demonstrate heretofore unde-scribed adaptations underlying the reversal of NAFLD by KD: That is, markedly altered hepatic mitochondrial fluxes and redox state to promote ketogenesis rather than synthesis of IHTG.
  • Raatevaara, Antti; Korpunen, Heikki; Tiitta, Markku; Tomppo, Laura; Kulju, Sampo; Antikainen, Jukka; Uusitalo, Jori (2020)
    Scots pine (Pinus sylvestris L.) heartwood is naturally durable wood material which has not been fully utilized in the wood industry. Currently, there are no practical measurement methods for detecting and measuring heartwood in a tree harvesting. The objective of this study was to evaluate the applicability of an electrical impedance spectroscopy and an image analysis of a log end face for pine heartwood measurements from the harvesting perspective. Both methods were tested with a fresh wood material which was collected during the harvesting operations. The results indicate that both methods have potential to measure the heartwood from processed stems with an average heartwood diameter error being less than two centimeters for each method. However, the image analysis of the log end face is only appropriate when visible contrast between the heartwood and a sapwood exists. Our findings indicate that the studied heartwood detection methods show great potential in measuring the heartwood of the stem in the harvesting phase which would ideally benefit later links in wood value chains.
  • Mynttinen, Elsi; Wester, Niklas; Lilius, Tuomas; Kalso, Eija; Mikladal, Bjorn; Varjos, Ilkka; Sainio, Sami; Jiang, Hua; Kauppinen, Esko I.; Koskinen, Jari; Laurila, Tomi (2020)
    Oxycodone is a strong opioid frequently used as an analgesic. Although proven efficacious in the management of moderate to severe acute pain and cancer pain, use of oxycodone imposes a risk of adverse effects such as addiction, overdose, and death. Fast and accurate determination of oxycodone blood concentration would enable personalized dosing and monitoring of the analgesic as well as quick diagnostics of possible overdose in emergency care. However, in addition to the parent drug, several metabolites are always present in the blood after a dose of oxycodone, and to date, there is no electrochemical data available on any of these metabolites. In this paper, a single-walled carbon nanotube (SWCNT) electrode and a Nafion-coated SWCNT electrode were used, for the first time, to study the electrochemical behavior of oxycodone and its two main metabolites, noroxycodone and oxymorphone. Both electrode types could selectively detect oxycodone in the presence of noroxycodone and oxymorphone. However, we have previously shown that addition of a Nafion coating on top of the SWCNT electrode is essential for direct measurements in complex biological matrices. Thus, the Nafion/SWCNT electrode was further characterized and used for measuring clinically relevant concentrations of oxycodone in buffer solution. The limit of detection for oxycodone with the Nafion/SWCNT sensor was 85 nM, and the linear range was 0.5-10 mu M in buffer solution. This study shows that the fabricated Nafion/SWCNT sensor has potential to be applied in clinical concentration measurements.
  • Suomivuori, Carl-Mikael; Gamiz-Hernandez, Ana P.; Sundholm, Dage; Kaila, Ville R. I. (2017)
    The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na+ pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521: 48-53]. To elucidate its molecular mechanism for Na+ pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na+ binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.