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  • 1.
    Andersson, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Thermal conductivity of normal and deuterated water, crystalline ice, and amorphous ices2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 149, no 12, article id 124506Article in journal (Refereed)
    Abstract [en]

    The effect of deuteration on the thermal conductivity kappa of water, crystalline ice, and amorphous ices was studied using the pressure induced amorphization of hexagonal ice, ice Ih, to obtain the deuterated, D2O, forms of low-density amorphous (LDA), high-density amorphous (HDA), and very-high density amorphous (VHDA) ices. Upon deuteration, kappa of ice Ih decreases between 3% and 4% in the 100-270 K range at ambient pressure, but the effect diminishes on densification at 130 K and vanishes just prior to amorphization near 0.8 GPa. The unusual negative value of the isothermal density rho dependence of kappa for ice Ih, g = (d ln kappa/d ln rho)(T) = -4.4, is less so for deuterated ice: g = -3.8. In the case of the amorphous ices and liquid water, kappa of water decreases by 3.5% upon deuteration at ambient conditions, whereas K of HDA and VHDA ices instead increases by up to 5% for pressures up to 1.2 GPa at 130 K, despite HDA's and VHDA's structural similarities with water. The results are consistent with significant heat transport by librational modes in amorphous ices as well as water, and that deuteration increases phonon-phonon scattering in crystalline ice. Heat transport by librational modes is more pronounced in D2O than in H2O at low temperatures due to a deuteration-induced red-shift of librational mode frequencies. Moreover, the results show that kappa of deuterated LDA ice is 4% larger than that of normal LDA at 130 K, and both forms display an unusual temperature dependence of kappa, which is reminiscent of that for crystals (kappa similar to T (-1)), and a unique negative pressure dependence of kappa, which likely is linked to local-order structural similarities to ice Ih. 

  • 2.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Carvalho, Paulo H. B. Brant
    Hsu, Ying-Jui
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Haussermann, Ulrich
    Transitions in pressure-amorphized clathrate hydrates akin to those of amorphous ices2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 151, no 1, article id 014502Article in journal (Refereed)
    Abstract [en]

    Type II clathrate hydrates (CHs) were studied by thermal and dielectric measurements. All CHs amorphize, or collapse, on pressurization to 1.3 GPa below 135 K. After heating to 160 K at 1 GPa, the stability of the amorphous states increases in a process similar to the gradual high density to very high density amorphous ice (HDA to VHDA) transition. On a subsequent pressure decrease, the amorphized CHs expand partly irreversibly similar to the gradual VHDA to expanded HDA ice transformation. After further heating at 1 GPa, weak transition features appear near the HDA to low density amorphous ice transition. The results suggest that CH nucleation sites vanish on heating to 160 K at 1 GPa and that a sluggish partial phase-separation process commences on further heating. The collapsed CHs show two glass transitions (GTs), GT1 and GT2. GT1 is weakly pressure-dependent, 12 K GPa(-1), with a relaxation time of 0.3 s at 140 K and 1 GPa; it is associated with a weak heat capacity increase of 3.7 J H2O-mol(-1) K-1 in a 18 K range and an activation energy of only 38 kJ mol(-1) at 1 GPa. The corresponding temperature of GT2 is 159 K at 0.4 GPa with a pressure dependence of 36 K GPa(-1); it shows 5.5 times larger heat capacity increase and 4 times higher activation energy than GT1. GT1 is observed also in HDA and VHDA, whereas GT2 occurs just above the crystallization temperature of expanded HDA and only within its similar to 0.2-0.7 GPa stable pressure range.

  • 3.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Inaba, Akira
    Unusual Grüneisen and Bridgman parameters of low-density amorphous ice and their implications on pressure induced amorphization2005In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 122, no 12, p. 124710-Article in journal (Refereed)
    Abstract [en]

    The low-temperature limiting value of the Grüneisen parameter for low-frequency phonons and the density dependence of the thermal conductivity (Bridgman parameter) of low-density amorphous (LDA) ice, high-density amorphous (HDA) ice, hexagonal ice Ih, and cubic ice Ic were calculated from high-pressure sound velocity and thermal conductivity measurements, yielding negative values for all states except HDA ice. LDA ice is the first amorphous state to exhibit a negative Bridgman parameter, and negative Grüneisen parameters are relatively unusual. Since Ih, Ic, and LDA ice all transform to HDA upon pressurization at low temperatures and share the unusual feature of negative Grüneisen parameters, this seems to be a prerequisite for pressure induced amorphization. We estimate that the Grüneisen parameter increases at the ice Ih to XI transition, and may become positive in ice XI, which indicates that proton-ordered ice XI does not amorphize like ice Ih on pressurization.

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  • 4.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, G P
    Sub-Tg features of glasses formed by cooling glycerol under pressure – Additional incompatibility of vibrational with configurational states in the depressurized, high density glass2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 145, article id 204506Article in journal (Refereed)
    Abstract [en]

    The vibrational state of a glass is naturally incompatible with its configurational state, which makes the glass structurally unstable. When a glass is kept at constant temperature, both the vibrational and configurational states of a glass change with time until it becomes metastable (equilibrium) liquid and the two states become compatible. The process, known as structural relaxation, occurs at a progressively higher rate during heating, and the properties of a glass change accordingly. We add to this incompatibility by depressurizing a glass that had been formed by cooling a liquid under a high pressure, p, and then investigate the effects of the added incompatibility by studying thermal conductivity, κ, and the heat capacity per unit volume ρCp of the depressurized glass.We use glycerol for the purpose and study first the changes in the features of κ and of ρCp during glass formation oncooling under a set of different p. We then partially depressurize the glass and study the effect of the p-induced instability on the features of and Cp as the glass is isobarically heated to the liquid state.At a given low p, the glass configuration that was formed by cooling at high-p had a higher κ than the glass configuration that was formed by cooling at a low p. The difference is more when the glass is formed at a higher p and/or is depressurized to a lower p. On heating at a low p, its κ decreases before its glass-liquid transition range is reached. The effect is the opposite of the increase in observed on heating a glass at the same p under which it was formed. It is caused by thermally assisted loss of the added incompatibility of configurational and vibrational states of a high-p formed glass kept at low p. If a glass formed under a low-p is pressurized and then heated under high p, it would show the opposite effect, i.e., its κ would first increase to its high p value before its glass-to-liquid transition range.

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  • 5.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P
    Effect of pressure on thermal conductivity and pressure collapse of ice in a polymer-hydrogel and kinetic unfreezing at 1 GPa2011In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 134, no 12, p. 124903-Article in journal (Refereed)
    Abstract [en]

    We report a study of aqueous solutions of poly(vinylalcohol) and its hydrogel by thermal conductivity,κ, and specific heat measurements. In particular, we investigate (i) the changes in the solution and the hydrogel at 0.1 MPa observed in the 350-90 K range and of the frozen hydrogel at 130 K observed in the range from 0.1 MPa to 1.3 GPa, and (ii) the nature of the pressure collapse of ice in the frozen hydrogel and kinetic unfreezing on heating of its high density water at 1 GPa. The water component of the polymer solution on cooling either first phase separates and then freezes to hexagonal ice or freezes without phase separation and the dispersed polymer chains freeze-concentrate in nanoscopic and microscopic regions of the grain boundaries and grain junctions of the ice crystals in the frozen state of water in the hydrogel. The change in κ with temperature at 1 bar is reversible with some hysteresis, but not reversible with pressure after compression to 0.8 GPa at 130 K. At high pressures the crystallized state collapses showing features of. and specific heat characteristic of formation of high density amorphous solid water. The pressure of structural collapse is 0.08 GPa higher than that of ice at 130 K. The slowly formed collapsed state shows kinetic unfreezing or glass-liquid transition temperature at 140 K for a time scale of 1 s. Comparison with the change in the properties observed for ice shows that κ decreases when the polymer is added. 

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  • 6.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P.
    Nature of the pressure-induced collapse of an ice clathrate by dielectric spectroscopy2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 129, no 23, article id 234505Article in journal (Refereed)
    Abstract [en]

    Collapse of an ice clathrate of type II structure containing tetrahydrofuran as guest molecules has been studied at different pressures by dielectric spectroscopy. The sample was pressurized to 1.3 GPa at 130 K and the resulting collapsed state was pressure cycled. The dielectric relaxation time increases at a progressively rapid rate during pressurizing and then decreases slowly on depressurizing, but the dielectric relaxation time does not reach the value of the original state. With increase in pressure, the limiting high frequency permittivity due to orientation of H2O molecules first increases by about 5% until 0.75 GPa and then decreases slightly until 1 GPa, and finally it increases until ~1.2 GPa. The decrease is attributed to the loss of contribution from the reorientational motion of tetrahydrofuran molecules and the increase to densification as the structure mechanically collapses completely in the 1–1.25 GPa range. The relaxation time of the collapsed state is comparable with that of the high-density amorph formed on pressure collapse of ice.

  • 7.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P
    Department of Materials Science and Engineering, McMaster University, Hamilton, Canada.
    Pressure-induced collapse of ice clathrate and hexagonal ice mixtures formed by freezing2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 131, p. 114503-114513Article in journal (Refereed)
    Abstract [en]

    We report thermal conductivity κ measurements of the pressure-induced collapse of two mixtures of ice and tetrahydrofuran (THF) clathrate hydrate formed by freezing aqueous solutions, THF·23 H2O and THF·20 H2O, one containing twice as much excess water than the other. On pressurizing, κ of the solid mixture first decreases at the onset pressure of 0.8 GPa, as occurs for collapse of pure ice, reaches a local minimum at a pressure of 1.0 GPa, and then increases as occurs for the collapse of the pure clathrate THF·17 H2O. This shows that in the apparently homogeneous mixture, the ice and the clathrate collapse as if the two were in a mechanically mixed state. The manner in which the clathrate aggregate can arrange in the solid indicates that ice occupies the interstitial space in the tightly packed aggregates and H2O molecules belonging to the lattice of one form hydrogen bond with that of the other, a feature that is preserved in their collapsed states. On decompression, the original clathrate is partially recovered in the THF·20 H2O mixture, but the collapsed ice does not transform to the low density amorph. We surmise that on irreversible transformation to the original clathrate, the aggregates expand. Any pressure thus exerted on the small domains of the collapsed ice with a hydrogen bonded interface with the clathrate aggregates could prevent it from transforming to the low density amorph. Measurements of κ are useful in investigating structural collapse of crystals when dilatometry is unable to do so, as κ seems to be more sensitive to pressure-induced changes than the volume.

  • 8.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P
    Spontaneous transformation of water's high-density amorph and a two-stage crystallization to ice VI at 1 GPa: a dielectric study2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 120, no 24, p. 11662-11671Article in journal (Refereed)
    Abstract [en]

    Dielectric relaxation spectra of a metastable crystal phase formed on implosive and exothermic transformation of pressure-amorphized hexagonal ice have been measured in situ at 0.97 GPa pressure over a range of temperature. The metastable phase showed no relaxation peak at 130 K and 0.97 GPa. When heated at a fixed pressure of 0.97 GPa, it began to transform at ∼ 145 K exothermally to a phase whose relaxation rate and equilibrium dielectric permittivity increased. A second, but slower exothermic transformation also occurred at ∼ 175 K. After keeping at 213 K, the relaxation rate and equilibrium permittivity reached the known values of these two quantities for ice VI. Thus the metastable phase transformed to ice VI in two stages. It is conjectured that the intermediate phase in this transformation could be ice XII. The rate of transformation is not determined by the reorientational relaxation rate of water molecules in the ices

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  • 9.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P.
    Department of Materials Science and Engineering, McMaster University, Hamilton, Ontario, Canada.
    Thermal conductivity of Glycerol’s liquid, glass, and crystal states, glass-liquid-glass transition, and crystallization at high pressures2016In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 144, article id 064504Article in journal (Refereed)
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  • 10.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P
    Time-dependent amorphization of ice at 0.8-0.9 GPa2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 121, no 8, p. 3936-3938Article in journal (Refereed)
    Abstract [en]

    Thermal conductivity measurements show that ice continues to amorphize for several days when kept at a fixed pressure p in the 0.79–0.88 GPa range, and fixed temperature T in the 127–130 K range. Thermal conductivity k decreases according to a stretched exponential in time, and its limiting long time value k() varies with p and T. At 0.8 GPa and 128 K, k() remains 2.5 times the value observed for high-density amorph. Consequences of these findings for our understanding of amorphization are discussed.

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  • 11.
    Andersson, Ove
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Johari, Gyan P
    Suga, H.
    An ice phase of lowest thermal conductivity2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 120, no 20, p. 9612-9617Article in journal (Refereed)
    Abstract [en]

    On pressurizing at temperatures near 130 K, hexagonal and cubic ices transform implosively at 0.8–1 GPa. The phase produced on transformation has the lowest thermal conductivity among the known crystalline ices and its value decreases on increase in temperature. An ice phase of similar thermal conductivity is produced also when high-density amorphous ice kept at 1 GPa transforms on slow heating when the temperature reaches ∼155 K. These unusual formation conditions, the density and its distinguished thermal conductivity, all indicate that a distinct crystal phase of ice has been produced.

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  • 12. Belorizky, Elie
    et al.
    Fries, Pascal H
    Helm, Lothar
    Kowalewski, Jozef
    Kruk, Danuta
    Sharp, Robert R
    Westlund, Per-Olof
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Comparison of different methods for calculating the paramagnetic relaxation enhancement of nuclear spins as a function of the magnetic field2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 5, article id 052315Article in journal (Refereed)
    Abstract [en]

    The enhancement of the spin-lattice relaxation rate for nuclear spins in a ligand bound to a paramagnetic metal ion [known as the paramagnetic relaxation enhancement (PRE)] arises primarily through the dipole-dipole (DD) interaction between the nuclear spins and the electron spins. In solution, the DD interaction is modulated mostly by reorientation of the nuclear spin-electron spin axis and by electron spin relaxation. Calculations of the PRE are in general complicated, mainly because the electron spin interacts so strongly with the other degrees of freedom that its relaxation cannot be described by second-order perturbation theory or the Redfield theory. Three approaches to resolve this problem exist in the literature: The so-called slow-motion theory, originating from Swedish groups [Benetis et al., Mol. Phys. 48, 329 (1983); Kowalewski et al., Adv. Inorg. Chem. 57, (2005); Larsson et al., J. Chem. Phys. 101, 1116 (1994); T. Nilsson et al., J. Magn. Reson. 154, 269 (2002)] and two different methods based on simulations of the dynamics of electron spin in time domain, developed in Grenoble [Fries and Belorizky, J. Chem. Phys. 126, 204503 (2007); Rast et al., ibid. 115, 7554 (2001)] and Ann Arbor [Abernathy and Sharp, J. Chem. Phys. 106, 9032 (1997); Schaefle and Sharp, ibid. 121, 5387 (2004); Schaefle and Sharp, J. Magn. Reson. 176, 160 (2005)], respectively. In this paper, we report a numerical comparison of the three methods for a large variety of parameter sets, meant to correspond to large and small complexes of gadolinium(III) and of nickel(II). It is found that the agreement between the Swedish and the Grenoble approaches is very good for practically all parameter sets, while the predictions of the Ann Arbor model are similar in a number of the calculations but deviate significantly in others, reflecting in part differences in the treatment of electron spin relaxation. The origins of the discrepancies are discussed briefly.

  • 13.
    Björnham, Oscar
    et al.
    Umeå University, Faculty of Science and Technology, Applied Physics and Electronics.
    Axner, Ove
    Umeå University, Faculty of Science and Technology, Physics.
    Multipili Attachment of Bacteria with Helix–like Pili Exposed to Stress2009In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 130, p. 235102-Article in journal (Refereed)
    Abstract [en]

    A number of biomechanical properties of various types of pili expressed by Escherichia coli, predominantly their force–vs.–elongation behavior, have previously been assessed in detail on a single pilus level. In vivo, however, bacteria bind in general to host cells by a multitude of pili, which presumably provides them with adhesion properties that differs from those of single pili. Based upon the previously assessed biomechanical properties of individual pili, this work presents a theoretical analysis of the adhesion properties of multipili–attaching bacteria expressing helix–like pili exposed to an external force. Expressions for the adhesion lifetime of dual– and multipili–attaching bacteria are derived and their validity is verified by Monte Carlo simulations. It is shown that the adhesion lifetime of a multipili–binding bacterium depends to a large degree on the cooperativity of the attaching pili, which, in turn, depends strongly on their internal biomechanical properties, in particular their helix–like structure and its ability to elongate, which, in turn, depend on the intrinsic properties of the bonds, e.g. their lengths and activation energies. It is shown, for example, that a decrease in the length of a layer–to–layer bond in the rod of P pili, expressed by E. coli, by 50 % leads to a decrease in the adhesion lifetime of a bacterium attaching by 10 pili and exposed to a force of 500 pN by three orders of magnitude. The results indicate moreover that the intrinsic properties of the rod for this particular type of pili are optimized for multipili attachment under a broad range of external forces and presumably also to its in vivo environment. Even though the results presented in this work apply quantitatively to one type of pilus, they are assumed to apply qualitatively to all helix–like pili systems expressing slip bonds.

  • 14. Carvalho, Paulo H. B. Brant
    et al.
    Mace, Amber
    Bull, Craig L.
    Funnell, Nicholas P.
    Tulk, Chris A.
    Andersson, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Häussermann, Ulrich
    Elucidation of the pressure induced amorphization of tetrahydrofuran clathrate hydrate2019In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 150, no 20, article id 204506Article in journal (Refereed)
    Abstract [en]

    The type II clathrate hydrate (CH) THF·17 H2O (THF = tetrahydrofuran) is known to amorphize on pressurization to ∼1.3 GPa in the temperature range 77–140 K. This seems to be related to the pressure induced amorphization (PIA) of hexagonal ice to high density amorphous (HDA) ice. Here, we probe the PIA of THF-d8 · 17 D2O (TDF-CD) at 130 K by in situthermal conductivity and neutron diffraction experiments. Both methods reveal amorphization of TDF-CD between 1.1 and 1.2 GPa and densification of the amorphous state on subsequent heating from 130 to 170 K. The densification is similar to the transition of HDA to very-high-density-amorphous ice. The first diffraction peak (FDP) of the neutron structure factor function, S(Q), of amorphous TDF-CD at 130 K appeared split. This feature is considered a general phenomenon of the crystalline to amorphous transition of CHs and reflects different length scales for D-D and D-O correlations in the water network and the cavity structure around the guest. The maximum corresponding to water-water correlations relates to the position of the FDP of HDA ice at ∼1 GPa. Upon annealing, the different length scales for water-water and water-guest correlations equalize and the FDP in the S(Q) of the annealed amorph represents a single peak. The similarity of local water structures in amorphous CHs and amorphous ices at in situ conditions is confirmed from molecular dynamics simulations. In addition, these simulations show that THF guest molecules are immobilized and retain long-range correlations as in the crystal.

  • 15.
    Castelain, Mickaël
    et al.
    Laboratoire de Rhéologie.
    Pignon, Frédéric
    Laboratoire de Rhéologie.
    Piau, Jean-Michel
    Laboratoire de Rhéologie.
    Magnin, Albert
    Laboratoire de Rhéologie.
    The initial single yeast cell adhesion on glass via optical trapping and Derjaguin-Landau-Verwey-Overbeek predictions.2008In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 128, no 13, p. 135101-Article in journal (Refereed)
    Abstract [en]

    We used an optical tweezer to investigate the adhesion of yeast Saccharomyces cerevisiae onto a glass substrate at the initial contact. Micromanipulation of free-living objects with single-beam gradient optical trap enabled to highlight mechanisms involved in this initial contact. As a function of the ionic strength and with a displacement parallel to the glass surface, the yeast adheres following different successive ways: (i) Slipping and rolling at 1.5 mM NaCl, (ii) slipping, rolling, and sticking at 15 mM NaCl, and (iii) only sticking at 150 mM. These observations were numerous and reproducible. A kinetic evolution of these adhesion phenomena during yeast movement was clearly established. The nature, range, and relative intensity of forces involved in these different adhesion mechanisms have been worked out as a quantitative analysis from Derjaguin-Landau-Verwey-Overbeek (DLVO) and extended DLVO theories. Calculations show that the adhesion mechanisms observed and their affinity with ionic strength were mainly governed by the Lifshitz-van der Waals interaction forces and the electrical double-layer repulsion to which are added specific contact forces linked to "sticky" glycoprotein secretion, considered to be the main forces capable of overcoming the short-range Lewis acid-base repulsions.

  • 16.
    Forsling, Robin
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Sanders, Lloyd P.
    Department of Astronomy and Theoretical Physics, Lund University, Sweden .
    Ambjörnsson, Tobias
    Department of Astronomy and Theoretical Physics, Lund University, Sweden .
    Lizana, Ludvig
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Non-Markovian effects in the first-passage dynamics of obstructed tracer particle diffusion in one-dimensional systems2014In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 9, p. 094902-Article in journal (Refereed)
    Abstract [en]

    The standard setup for single-file diffusion is diffusing particles in one dimension which cannot overtake each other, where the dynamics of a tracer (tagged) particle is of main interest. In this article, we generalize this system and investigate first-passage properties of a tracer particle when flanked by identical crowder particles which may, besides diffuse, unbind (rebind) from (to) the one-dimensional lattice with rates k(off) (k(on)). The tracer particle is restricted to diffuse with rate k(D) on the lattice and the density of crowders is constant (on average). The unbinding rate k(off) is our key parameter and it allows us to systematically study the non-trivial transition between the completely Markovian case (k(off) >> k(D)) to the non-Markovian case (k(off) << k(D)) governed by strong memory effects. This has relevance for several quasi one-dimensional systems. One example is gene regulation where regulatory proteins are searching for specific binding sites on a crowded DNA. We quantify the first-passage time distribution, f(t) (t is time), numerically using the Gillespie algorithm, and estimate f(t) analytically. In terms of k(off) (keeping k(D) fixed), we study the transition between the two known regimes: (i) when k(off) >> k(D) the particles may effectively pass each other and we recover the single particle result f(t) similar to t(-3/2), with a reduced diffusion constant; (ii) when k(off) << k(D) unbinding is rare and we obtain the single-file result f (t) similar to t(-7/4). The intermediate region displays rich dynamics where both the characteristic f (t) - peak and the long-time power-law slope are sensitive to k(off).

  • 17.
    Hashemloo, Avazeh
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Dion, Claude
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Rotational dynamics of a diatomic molecular ion in a Paul trap2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, article id 204308Article in journal (Refereed)
    Abstract [en]

    We present models for a heteronuclear diatomic molecular ion in a linear Paul trap in a rigid-rotor approximation, one purely classical and the other where the center-of-mass motion is treated classically, while rotational motion is quantized. We study the rotational dynamics and their influenceon the motion of the center-of-mass, in the presence of the coupling between the permanent dipole moment of the ion and the trapping electric field. We show that the presence of the permanent dipole moment affects the trajectory of the ion and that it departs from the Mathieu equation solution found for atomic ions. For the case of quantum rotations, we also evidence the effect of the above-mentioned coupling on the rotational states of the ion.

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  • 18. Inaba, Akira
    et al.
    Matsuo, Takasuke
    Fransson, Åke
    Umeå University, Faculty of Science and Technology, Applied Physics and Electronics.
    Sundqvist, Bertil
    Umeå University, Faculty of Science and Technology, Physics.
    Lattice vibrations and thermodynamic stability of polymerized C60 deduced from heat capacities1999In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 110, no 24, p. 12226-12232Article in journal (Refereed)
    Abstract [en]

    Heat capacities of 1D and 2D pressure polymerized C60 as well as the thermally depolymerized C60 have been measured at temperatures between 4 and 350 K and the results analyzed for the lattice vibrations and the thermodynamic stability. It was found from the low-temperature heat capacity (T < 100 K) that on polymerization (1) the lattice vibrations, both translational and rotational, stiffen substantially, (2) an anisotropic nature emerges in response to the lower dimensionality, and (3) an anharmonicity still remains as in pristine C60. The normal C60 has an excess entropy of 67.8 and 99.4 J K – 1 mol – 1 at 300 K relative to the 1D and 2D polymerized C60, respectively. The thermodynamic stability is considered with two possible phase diagrams.

  • 19.
    Inaba, Akira
    et al.
    Osaka, Japan.
    Miyazaki, Yuji
    Osaka, Japan.
    Michalowski, Pawel P.
    Warsaw, Poland.
    Gracia-Espino, Eduardo
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Sundqvist, Bertil
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Calorimetric measurements on Li4C60 and Na4C602015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 142, no 16, article id 164706Article in journal (Refereed)
    Abstract [en]

    We show specific heat data for Na4C60 and Li4C60 in the range 0.4-350 K for samples characterized by Raman spectroscopy and X-ray diffraction. At high temperatures, the two different polymer structures have very similar specific heats both in absolute values and in general trend. The specific heat data are compared with data for undoped polymeric and pristine C60. At high temperatures, a difference in specific heat between the intercalated and undoped C60 polymers of 100 J K−1 mol−1 is observed, in agreement with the Dulong-Petit law. At low temperatures, the specific heat data for Li4C60 and Na4C60 are modified by the stiffening of vibrational and librational molecular motion induced by the polymer bonds. The covalent twin bonds in Li4C60 affect these motions to a somewhat higher degree than the single intermolecular bonds in Na4C60. Below 1 K, the specific heats ofboth materials become linear in temperature, as expected from the effective dimensionality of the structure. The contribution to the total specific heat from the inserted metal ions can be well described by Einstein functions with TE = 386 K for Li4C60 and TE = 120 K for Na4C60, but for both materials we also observe a Schottky-type contribution corresponding to a first approximation to a two-level system with ΔE = 9.3 meV for Li4C60 and 3.1 meV for Na4C60, probably associated with jumps between closely spaced energy levels inside “octahedral-type” ionic sites. Static magnetic fields up to 9 T had very small effects on the specific heat below 10 K.

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  • 20. Johari, G. P.
    et al.
    Andersson, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Effects of stacking disorder on thermal conductivity of cubic ice2015In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 143, no 5, article id 054505Article in journal (Refereed)
    Abstract [en]

    Cubic ice is said to have stacking disorder when the H2O sequences in its structure (space group Fd (3) over barm) are interlaced with hexagonal ice (space group P6(3)/mmc) sequences, known as stacking faults. Diffraction methods have shown that the extent of this disorder varies in samples made by different methods, thermal history, and the temperature T, but other physical properties of cubic and hexagonal ices barely differ. We had found that at 160 K, the thermal conductivity, kappa, of cubic ice is similar to 20% less than that of hexagonal ice, and this difference varies for cubic ice samples prepared by different methods and/or subjected to different thermal history. After reviewing the methods of forming cubic ice, we report an investigation of the effects of stacking disorder and other features by using new data, and by analyzing our previous data on the dependence of kappa on T and on the pressure. We conclude that the lower kappa of cubic ice and its weaker T-dependence is due mainly to stacking disorder and small crystal sizes. On in situ heating at 20-50 MPa pressure, kappa increases and cubic ice irreversibly transforms more sharply to ice Ih, and at a higher T of similar to 220 K, than it does in ex situ studies. Cooling and heating between 115 and 130 K at 0.1 K min(-1) rate yield the same kappa value, indicating that the state of cubic ice in these conditions does not change with time and T. The increase in kappa of cubic ice observed on heat-annealing before its conversion to hexagonal ice is attributed to the loss of stacking faults and other types of disorders, and to grain growth. After discussing the consequences of our findings on other properties, we suggest that detailed studies of variation of a given property of cubic ice with the fraction of stacking faults in its structure may reveal more about the effect of this disorder. A similar disorder may occur in the mono-layers of H2O adsorbed on a substrate, in bulk materials comprised of two dimensional layers, in diamond and in Zirconium and in numerous other crystals.

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  • 21. Johari, G. P.
    et al.
    Andersson, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Structural relaxation and thermal conductivity of high-pressure formed, high-density di-n-butyl phthalate glass and pressure induced departures from equilibrium state2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 146, no 23, article id 234505Article in journal (Refereed)
    Abstract [en]

    We report a study of structural relaxation of high-density glasses of di-n-butyl phthalate (DBP) by measuring thermal conductivity, κ, under conditions of pressure and temperature (p,T) designed to modify both the vibrational and configurational states of a glass. Various high-density glassy states of DBP were formed by (i) cooling the liquid under a fixed high p and partially depressurizing the glass, (ii) isothermal annealing of the depressurized glass, and (iii) pressurizing the glass formed by cooling the liquid under low p. At a given low p, κ of the glass formed by cooling under high p is higher than that of the glass formed by cooling under low p, and the difference increases as glass formation p is increased. κ of the glass formed under 1 GPa is ∼20% higher at ambient p than κ of the glass formed at ambient p. On heating at low p, κ decreases until the glass to liquid transition range is reached. This is the opposite of the increase in κ observed when a glass formed under a certain p is heated under the same p. At a given high p, κ of the low-density glass formed by cooling at low p is lower than that of the high-density glass formed by cooling at that high p. On heating at high p, κ increases until the glass to liquid transition range is reached. The effects observed are due to a thermally assisted approach toward equilibrium at p different from the glass formation p. In all cases, the density, enthalpy, and entropy would change until the glasses become metastable liquids at a fixed p, thus qualitatively relating κ to variation in these properties.

  • 22. Johari, G. P.
    et al.
    Andersson, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Sundqvist, Bertil
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Instability and thermal conductivity of pressure-densified and elastically altered orientational glass of Buckminsterfullerene2018In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 148, no 14, article id 144502Article in journal (Refereed)
    Abstract [en]

    We report on the temperature, pressure and time (T, p and t)- dependent features of thermal conductivity, k, of partially ordered, non-equilibrium state of C60-OG, the orientational glass of Buckminsterfullerene (at T below the orientational freezing temperature Tog) made more unstable (i) by partially depressurizing its high-p formed state to elastically expand it, and (ii) by further pressurizing that state to elastically contract it. The sub-Tog effects observed on heating of C60-OG differ from those of glasses, because phonon propagation depends on the ratio of two well-defined orientational states of C60 molecules and the density of the solid. A broad peak-like feature appears at T near Tog in the k-T plots of C60-OG formed at 0.7 and heated at 0.2 GPa, which we attribute to partial overlap of the sub-Tog and Tog features. A sub-Tog local minimum appears in the k -T plots at T well below Tog  of C60-OG formed at 0.1 GPa and heated at 0.5 GPa, and corresponds to the state of maximum disorder. Although Buckminsterfullerene is regarded as an orientationally-disordered crystal, variation of its properties with T and p is qualitatively different from other such crystals. We discuss the findings in terms of the nature of its disorder, sensitivity of its rotational dynamics to temperature and the absence of the Johari-Goldstein relaxation. All seem to affect the phenomenology of its glass-like transition.

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  • 23. Johari, Gyan P
    et al.
    Andersson, Ove
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Water's polyamorphic transitions and amorphization of ice under pressure2004In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 120, no 13, p. 6207-6213Article in journal (Refereed)
    Abstract [en]

    Transformations of water’s high density amorph (HDA) to low density amorph (LDA) and of LDA’s to cubic ice (Ic) have been studied by in situ thermal conductivity κ measurements at high pressures. The HDA to LDA transformation is unobservable at p of 0.07 GPa, indicating that, for a fixed heating rate, an increase in pressure increases the temperature of HDA to LDA transformation and decreases that of LDA to ice Ic, causing thereby the two transformations to merge, and HDA appears to convert directly to ice Ic. Thus either LDA forms but converts extremely rapidly to ice Ic, or LDA does not form. At a fixed p and T, in the range of pressure amorphization of hexagonal ice, κ continues to decrease with time. Therefore, the amorphization of ice Ih is kinetically controlled. When HDA at 1 GPa was heated from 130 to 157 K and densified to very HDA, its κ increased by 3%. Our findings and a scrutiny of earlier reports show that a reversible transition between HDA and LDA does not occur at ∼135 K and ∼0.2 GPa. Since there is no unique HDA, it is difficult to justify the conjecture for a second critical point for water.

  • 24. Kim, Y
    et al.
    Abou-Hamad, E
    Rubio, A
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Talyzin, Alexandr
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Boesch, D
    Aloni, S
    Zettl, A
    Luzi, D E
    Goze-Bac, C
    Communications: nanomagnetic shielding: high-resolution NMR in carbon allotropes2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, no 2, p. 021102-Article in journal (Refereed)
    Abstract [en]

    The understanding and control of the magnetic properties of carbon-based materials is of fundamental relevance in applications in nano- and biosciences. Ring currents do play a basic role in those systems. In particular the inner cavities of nanotubes offer an ideal environment to investigate the magnetism of synthetic materials at the nanoscale. Here, by means of 13 C high resolution NMR of encapsulated molecules in peapod hybrid materials, we report the  largest diamagnetic shifts (down to -68.3 ppm) ever observed in carbon allotropes, which is connected to the enhancement of the aromaticity of the nanotube envelope upon doping. This diamagnetic shift can be externally controlled by in situ modifications such as doping or electrostatic charging. Moreover, defects such as C-vacancies, pentagons, and chemical functionalization of the outer nanotube quench this diamagnetic effect and restore NMR signatures to slightly paramagnetic shifts compared to nonencapsulated molecules. The magnetic interactions reported here are robust phenomena independent of temperature and proportional to the applied magnetic field. The magnitude, tunability, and stability of the magnetic effects make the peapod nanomaterials potentially valuable for nanomagnetic shielding in nanoelectronics and nanobiomedical engineering.

  • 25.
    Kim, Y
    et al.
    Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania.
    Abou-Hamad, Edy
    CNRS Université Montpellier 2, France .
    Rubio, Angelo
    European Theoretical Spectroscopy Facility (ETSF), Universidad del País Vasco UPV/EHU, Spain .
    Wågberg, Thomas
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Talyzin, Aleksandr V.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Boesch, D
    Department of Physics, University of California, Berkeley, California 94720 USA and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA .
    Aloni, S
    Department of Physics, University of California, Berkeley, California 94720 USA and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA .
    Zettl, Alex
    Department of Physics, University of California, Berkeley, California 94720 USA and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA .
    Luzzi, David E.
    Department of Materials Science and Engineering, University of Pennsylvania, USA .
    Goze-Bac, Christophe
    CNRS Université Montpellier 2, France .
    Nanomagnetic shielding: High-resolution NMR in carbon allotropes2010In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 132, p. 021102-Article in journal (Refereed)
    Abstract [en]

    Theunderstanding and control of the magnetic properties of carbon-based materialsis of fundamental relevance in applications in nano- and biosciences.Ring currents do play a basic role in those systems.In particular the inner cavities of nanotubes offer an idealenvironment to investigate the magnetism of synthetic materials at thenanoscale. Here, by means of 13C high resolution NMR ofencapsulated molecules in peapod hybrid materials, we report the largestdiamagnetic shifts (down to −68.3 ppm) ever observed in carbonallotropes, which is connected to the enhancement of the aromaticityof the nanotube envelope upon doping. This diamagnetic shift canbe externally controlled by in situ modifications such as dopingor electrostatic charging. Moreover, defects such as C-vacancies, pentagons, andchemical functionalization of the outer nanotube quench this diamagnetic effectand restore NMR signatures to slightly paramagnetic shifts compared tononencapsulated molecules. The magnetic interactions reported here are robust phenomenaindependent of temperature and proportional to the applied magnetic field.The magnitude, tunability, and stability of the magnetic effects makethe peapod nanomaterials potentially valuable for nanomagnetic shielding in nanoelectronicsand nanobiomedical engineering

  • 26. Okotrub, A V
    et al.
    Belavin , V V
    Bulusheva , LG
    Davydov, VA
    Makarova , TL
    Umeå University.
    Tomanek, D
    Electronic structure and properties of rhombohedrally polymerized C602001In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 115, no 12, p. 5637-5631Article in journal (Refereed)
  • 27.
    Ross, Russell George
    et al.
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Andersson, Per
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Bäckström, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Physics.
    Effects of H and D order on the thermal conductivity of ice phases1978In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 68, no 9, p. 3967-3972Article in journal (Refereed)
    Abstract [en]

    Thermal conductivities (λ) of nine ice phases were determined by the transient hot wire method in a temperature range of 100–300 K and under pressures up to 2.2 GPa. Pure D2O as well as D2O–H2O mixtures were found to have values of λ close to those of pure H2O, except in phase VIII. For this phase λ was found to be about 9% lower in the case of pure D2O as well as in 1:1 and 1:3 mixtures of D2O:H2O. The hydrogen ordered phases systematically exhibit higher λ than the disordered ones, and in particular the presence of ice VI′ could be detected by a change of slope at low T in the curve of ln λ versus ln T for phase VI. If the results are fitted to the function λ=CT−n, the values of n fall into two groups. One group with n<1 contains only paraelectric phases, whereas the other group, having higher values of n, contains antiferroelectric phases and phase Ih. The latter phase is exceptional in that λ has a negative pressure coefficient. The results are interpreted in terms of dynamic decoupling of the hydrogen atoms from the lattice and in terms of induced oxygen disorder.

  • 28. Wang, Qian
    et al.
    Christiansen, Alexander
    Samiotakis, Antonios
    Wittung-Stafshede, Pernilla
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Cheung, Margaret S.
    Comparison of chemical and thermal protein denaturation by combination of computational and experimental approaches. II2011In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 135, no 17, p. 175102-Article in journal (Refereed)
    Abstract [en]

    Chemical and thermal denaturation methods have been widely used to investigate folding processes of proteins in vitro. However, a molecular understanding of the relationship between these two perturbation methods is lacking. Here, we combined computational and experimental approaches to investigate denaturing effects on three structurally different proteins. We derived a linear relationship between thermal denaturation at temperature T(b) and chemical denaturation at another temperature T(u) using the stability change of a protein (Delta G). For this, we related the dependence of Delta G on temperature, in the Gibbs-Helmholtz equation, to that of Delta G on urea concentration in the linear extrapolation method, assuming that there is a temperature pair from the urea (T(u)) and the aqueous (T(b)) ensembles that produces the same protein structures. We tested this relationship on apoazurin, cytochrome c, and apoflavodoxin using coarse-grained molecular simulations. We found a linear correlation between the temperature for a particular structural ensemble in the absence of urea, T(b), and the temperature of the same structural ensemble at a specific urea concentration, T(u). The in silico results agreed with in vitro far-UV circular dichroism data on apoazurin and cytochrome c. We conclude that chemical and thermal unfolding processes correlate in terms of thermodynamics and structural ensembles at most conditions; however, deviations were found at high concentrations of denaturant.

    (C) 2011 American Institute of Physics. [doi: 10.1063/1.3656692]

  • 29. Yang, Guomin
    et al.
    Neretnieks, Ivars
    Holmboe, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores2017In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 147, no 8, article id 084705Article in journal (Refereed)
    Abstract [en]

    During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and about eight water molecules in the first hydration shell within a radius of 3.3 Å at all higher hydration states. Moreover, the MD results show that the complete hydration shells are nearly spherical with an orthogonal coordination sphere. They could only be formed when the basal spacing d001 ≥ 18.7 Å, i.e., approximately, the interlayer separation h ≥ 10 Å. Comparison between DFT and MD simulations shows that DFT failed to reproduce the outer-sphere complexes in the Stern-layer (within ∼5.0 Å from the clay basal-plane), observed in the MD simulations.

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