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1.
Nat Immunol ; 24(7): 1124-1137, 2023 07.
Artículo en Inglés | MEDLINE | ID: mdl-37217705

RESUMEN

The magnitude and quality of the germinal center (GC) response decline with age, resulting in poor vaccine-induced immunity in older individuals. A functional GC requires the co-ordination of multiple cell types across time and space, in particular across its two functionally distinct compartments: the light and dark zones. In aged mice, there is CXCR4-mediated mislocalization of T follicular helper (TFH) cells to the dark zone and a compressed network of follicular dendritic cells (FDCs) in the light zone. Here we show that TFH cell localization is critical for the quality of the antibody response and for the expansion of the FDC network upon immunization. The smaller GC and compressed FDC network in aged mice were corrected by provision of TFH cells that colocalize with FDCs using CXCR5. This demonstrates that the age-dependent defects in the GC response are reversible and shows that TFH cells support stromal cell responses to vaccines.


Asunto(s)
Linfocitos T Colaboradores-Inductores , Vacunas , Animales , Ratones , Linfocitos B , Células T Auxiliares Foliculares , Centro Germinal , Envejecimiento
2.
Chem Rev ; 116(13): 7529-50, 2016 07 13.
Artículo en Inglés | MEDLINE | ID: mdl-27049513

RESUMEN

Nuclear quantum effects influence the structure and dynamics of hydrogen-bonded systems, such as water, which impacts their observed properties with widely varying magnitudes. This review highlights the recent significant developments in the experiment, theory, and simulation of nuclear quantum effects in water. Novel experimental techniques, such as deep inelastic neutron scattering, now provide a detailed view of the role of nuclear quantum effects in water's properties. These have been combined with theoretical developments such as the introduction of the principle of competing quantum effects that allows the subtle interplay of water's quantum effects and their manifestation in experimental observables to be explained. We discuss how this principle has recently been used to explain the apparent dichotomy in water's isotope effects, which can range from very large to almost nonexistent depending on the property and conditions. We then review the latest major developments in simulation algorithms and theory that have enabled the efficient inclusion of nuclear quantum effects in molecular simulations, permitting their combination with on-the-fly evaluation of the potential energy surface using electronic structure theory. Finally, we identify current challenges and future opportunities in this area of research.

3.
Sensors (Basel) ; 18(10)2018 Oct 16.
Artículo en Inglés | MEDLINE | ID: mdl-30332821

RESUMEN

The oil and gas industry faces increasing pressure to remove people from dangerous offshore environments. Robots present a cost-effective and safe method for inspection, repair, and maintenance of topside and marine offshore infrastructure. In this work, we introduce a new multi-sensing platform, the Limpet, which is designed to be low-cost and highly manufacturable, and thus can be deployed in huge collectives for monitoring offshore platforms. The Limpet can be considered an instrument, where in abstract terms, an instrument is a device that transforms a physical variable of interest (measurand) into a form that is suitable for recording (measurement). The Limpet is designed to be part of the ORCA (Offshore Robotics for Certification of Assets) Hub System, which consists of the offshore assets and all the robots (Underwater Autonomous Vehicles, drones, mobile legged robots etc.) interacting with them. The Limpet comprises the sensing aspect of the ORCA Hub System. We integrated the Limpet with Robot Operating System (ROS), which allows it to interact with other robots in the ORCA Hub System. In this work, we demonstrate how the Limpet can be used to achieve real-time condition monitoring for offshore structures, by combining remote sensing with signal-processing techniques. We show an example of this approach for monitoring offshore wind turbines, by designing an experimental setup to mimic a wind turbine using a stepper motor and custom-designed acrylic fan blades. We use the distance sensor, which is a Time-of-Flight sensor, to achieve the monitoring process. We use two different approaches for the condition monitoring process: offline and online classification. We tested the offline classification approach using two different communication techniques: serial and Wi-Fi. We performed the online classification approach using two different communication techniques: LoRa and optical. We train our classifier offline and transfer its parameters to the Limpet for online classification. We simulated and classified four different faults in the operation of wind turbines. We tailored a data processing procedure for the gathered data and trained the Limpet to distinguish among each of the functioning states. The results show successful classification using the online approach, where the processing and analysis of the data is done on-board by the microcontroller. By using online classification, we reduce the information density of our transmissions, which allows us to substitute short-range high-bandwidth communication systems with low-bandwidth long-range communication systems. This work shines light on how robots can perform on-board signal processing and analysis to gain multi-functional sensing capabilities, improve their communication requirements, and monitor the structural health of equipment.

4.
Phys Chem Chem Phys ; 17(38): 24666-82, 2015 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-26204101

RESUMEN

Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes. We also consider the entanglement developed using adiabatic electronic basis, providing a novel way for interpreting effects of the breakdown of the Born-Oppenheimer (BO) approximation. We consider: (i) BO entanglement in the ground-state wavefunction relevant to equilibrium thermodynamics, (ii) BO entanglement associated with low-energy wavefunctions relevant to infrared and tunneling spectroscopies, (iii) BO entanglement in high-energy eigenfunctions relevant to chemical reaction processes, and (iv) BO entanglement developed during reactive wavepacket dynamics. A two-state single-mode diabatic model descriptive of a wide range of chemical phenomena is used for this purpose. The entanglement developed by BO breakdown correlates simply with the diameter of the cusp introduced by the BO approximation, and a hierarchy appears between the various BO-breakdown correction terms, with the first-derivative correction being more important than the second-derivative correction which is more important than the diagonal correction. This simplicity is in contrast to the complexity of BO-breakdown effects on thermodynamic, spectroscopic, and kinetic properties. Further, processes poorly treated at the BO level that appear adequately treated using the Born-Huang adiabatic approximation are found to have properties that can only be described using a non-adiabatic description. For the entanglement developed between diabatic electronic states and the nuclear motion, qualitatively differently behavior is found compared to traditional properties of the density matrix and hence entanglement provides new information about system properties. For chemical reactions, this type of entanglement simply builds up as the transition-state region is crossed. It is robust to small changes in parameter values and is therefore more attractive for making quantum qubits than is the related fragile ground-state entanglement, provided that coherent motion at the transition state can be sustained.


Asunto(s)
Modelos Químicos , Electrones , Cinética , Teoría Cuántica , Termodinámica , Vibración
5.
Phys Chem Chem Phys ; 17(38): 24598-617, 2015 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-26193994

RESUMEN

While diabatic approaches are ubiquitous for the understanding of electron-transfer reactions and have been mooted as being of general relevance, alternate applications have not been able to unify the same wide range of observed spectroscopic and kinetic properties. The cause of this is identified as the fundamentally different orbital configurations involved: charge-transfer phenomena involve typically either 1 or 3 electrons in two orbitals whereas most reactions are typically closed shell. As a result, two vibrationally coupled electronic states depict charge-transfer scenarios whereas three coupled states arise for closed-shell reactions of non-degenerate molecules and seven states for the reactions implicated in the aromaticity of benzene. Previous diabatic treatments of closed-shell processes have considered only two arbitrarily chosen states as being critical, mapping these states to those for electron transfer. We show that such effective two-state diabatic models are feasible but involve renormalized electronic coupling and vibrational coupling parameters, with this renormalization being property dependent. With this caveat, diabatic models are shown to provide excellent descriptions of the spectroscopy and kinetics of the ammonia inversion reaction, proton transfer in N2H7(+), and aromaticity in benzene. This allows for the development of a single simple theory that can semi-quantitatively describe all of these chemical phenomena, as well as of course electron-transfer reactions. It forms a basis for understanding many technologically relevant aspects of chemical reactions, condensed-matter physics, chemical quantum entanglement, nanotechnology, and natural or artificial solar energy capture and conversion.


Asunto(s)
Benceno/química , Modelos Químicos , Amoníaco/química , Transporte de Electrón , Electrones , Isomerismo , Cinética , Protones , Teoría Cuántica , Termodinámica
6.
Phys Chem Chem Phys ; 17(38): 24641-65, 2015 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-26196265

RESUMEN

Using a simple model Hamiltonian, the three correction terms for Born-Oppenheimer (BO) breakdown, the adiabatic diagonal correction (DC), the first-derivative momentum non-adiabatic correction (FD), and the second-derivative kinetic-energy non-adiabatic correction (SD), are shown to all contribute to thermodynamic and spectroscopic properties as well as to thermal non-diabatic chemical reaction rates. While DC often accounts for >80% of thermodynamic and spectroscopic property changes, the commonly used practice of including only the FD correction in kinetics calculations is rarely found to be adequate. For electron-transfer reactions not in the inverted region, the common physical picture that diabatic processes occur because of surface hopping at the transition state is proven inadequate as the DC acts first to block access, increasing the transition state energy by (ℏω)(2)λ/16J(2) (where λ is the reorganization energy, J the electronic coupling and ω the vibration frequency). However, the rate constant in the weakly-coupled Golden-Rule limit is identified as being only inversely proportional to this change rather than exponentially damped, owing to the effects of tunneling and surface hopping. Such weakly-coupled long-range electron-transfer processes should therefore not be described as "non-adiabatic" processes as they are easily described by Born-Huang ground-state adiabatic surfaces made by adding the DC to the BO surfaces; instead, they should be called just "non-Born-Oppenheimer" processes. The model system studied consists of two diabatic harmonic potential-energy surfaces coupled linearly through a single vibration, the "two-site Holstein model". Analytical expressions are derived for the BO breakdown terms, and the model is solved over a large parameter space focusing on both the lowest-energy spectroscopic transitions and the quantum dynamics of coherent-state wavepackets. BO breakdown is investigated pertinent to: ammonia inversion, aromaticity in benzene, the Creutz-Taube ion, the bacterial photosynthetic reaction centre, BNB, the molecular conductor Alq3, and inverted-region charge recombination in a ferrocene-porphyrin-fullerene triad photosynthetic model compound. Throughout, the fundamental nature of BO breakdown is linked to the properties of the cusp catastrophe: the cusp diameter is shown to determine the magnitudes of all couplings, numerical basis-set and trajectory-integration requirements, and to determine the transmission coefficient κ used to understand deviations from transition-state theory.


Asunto(s)
Modelos Químicos , Amoníaco/química , Benceno/química , Transporte de Electrón , Electrones , Cinética , Teoría Cuántica , Termodinámica
7.
Phys Chem Chem Phys ; 17(38): 24618-40, 2015 Oct 14.
Artículo en Inglés | MEDLINE | ID: mdl-26190514

RESUMEN

Ammonia adopts sp(3) hybridization (HNH bond angle 108°) whereas the other members of the XH3 series PH3, AsH3, SbH3, and BiH3 instead prefer octahedral bond angles of 90-93°. We use a recently developed general diabatic description for closed-shell chemical reactions, expanded to include Rydberg states, to understand the geometry, spectroscopy and inversion reaction profile of these molecules, fitting its parameters to results from Equation of Motion Coupled-Cluster Singles and Doubles (EOM-CCSD) calculations using large basis sets. Bands observed in the one-photon absorption spectrum of NH3 at 18.3 eV, 30 eV, and 33 eV are reassigned from Rydberg (formally forbidden) double excitations to valence single-excitation resonances. Critical to the analysis is the inclusion of all three electronic states in which two electrons are placed in the lone-pair orbital n and/or the symmetric valence σ* antibonding orbital. An illustrative effective two-state diabatic model is also developed containing just three parameters: the resonance energy driving the high-symmetry planar structure, the reorganization energy opposing it, and HXH bond angle in the absence of resonance. The diabatic orbitals are identified as sp hybrids on X; for the radical cations XH3(+) for which only 2 electronic states and one conical intersection are involved, the principle of orbital following dictates that the bond angle in the absence of resonance is acos(-1/5) = 101.5°. The multiple states and associated multiple conical intersection seams controlling the ground-state structure of XH3 renormalize this to acos[3 sin(2)(2(1/2)atan(1/2))/2 - 1/2] = 86.7°. Depending on the ratio of the resonance energy to the reorganization energy, equilibrium angles can vary from these limiting values up to 120°, and the anomalously large bond angle in NH3 arises because the resonance energy is unexpectedly large. This occurs as the ordering of the lowest Rydberg orbital and the σ* orbital swap, allowing Rydbergization to compresses σ* to significantly increase the resonance energy. Failure of both the traditional and revised versions of the valence-shell electron-pair repulsion (VSEPR) theory to explain the ground-state structures in simple terms is attributed to exclusion of this key physical interaction.


Asunto(s)
Amoníaco/química , Antimonio/química , Arsenicales/química , Modelos Químicos , Bismuto/química , Fósforo/química , Teoría Cuántica , Termodinámica
8.
J Chem Phys ; 143(4): 044309, 2015 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-26233131

RESUMEN

If a deuterated molecule containing strong intramolecular hydrogen bonds is placed in a hydrogenated solvent, it may preferentially exchange deuterium for hydrogen. This preference is due to the difference between the vibrational zero-point energy for hydrogen and deuterium. It is found that the associated fractionation factor Φ is correlated with the strength of the intramolecular hydrogen bonds. This correlation has been used to determine the length of the H-bonds (donor-acceptor separation) in a diverse range of enzymes and has been argued to support the existence of short low-barrier H-bonds. Starting with a potential energy surface based on a simple diabatic state model for H-bonds, we calculate Φ as a function of the proton donor-acceptor distance R. For numerical results, we use a parameterization of the model for symmetric O-H⋯O bonds [R. H. McKenzie, Chem. Phys. Lett. 535, 196 (2012)]. We consider the relative contributions of the O-H stretch vibration, O-H bend vibrations (both in plane and out of plane), tunneling splitting effects at finite temperature, and the secondary geometric isotope effect. We compare our total Φ as a function of R with NMR experimental results for enzymes, and in particular with an earlier model parametrization Φ(R), used previously to determine bond lengths.


Asunto(s)
Deuterio/química , Enlace de Hidrógeno , Proteínas/química , Termodinámica , Hidrógeno/química , Espectroscopía de Resonancia Magnética , Solventes/química
9.
J Chem Phys ; 142(8): 084502, 2015 Feb 28.
Artículo en Inglés | MEDLINE | ID: mdl-25725740

RESUMEN

We propose and analyze a two-state valence-bond model of non-equilibrium solvation effects on the excited-state twisting reaction of monomethine cyanines. Suppression of this reaction is thought responsible for environment-dependent fluorescence yield enhancement in these dyes. Fluorescence is quenched because twisting is accompanied via the formation of dark twisted intramolecular charge-transfer (TICT) states. For monomethine cyanines, where the ground state is a superposition of structures with different bond and charge localizations, there are two possible twisting pathways with different charge localizations in the excited state. For parameters corresponding to symmetric monomethines, the model predicts two low-energy twisting channels on the excited-state surface, which leads to a manifold of TICT states. For typical monomethines, twisting on the excited state surface will occur with a small barrier or no barrier. Changes in the solvation configuration can differentially stabilize TICT states in channels corresponding to different bonds, and that the position of a conical intersection between adiabatic states moves in response to solvation to stabilize either one channel or the other. There is a conical intersection seam that grows along the bottom of the excited-state potential with increasing solvent polarity. For monomethine cyanines with modest-sized terminal groups in moderately polar solution, the bottom of the excited-state potential surface is completely spanned by a conical intersection seam.

10.
J Chem Phys ; 141(10): 104314, 2014 Sep 14.
Artículo en Inglés | MEDLINE | ID: mdl-25217923

RESUMEN

Four diabatic states are used to construct a simple model for double proton transfer in hydrogen bonded complexes. Key parameters in the model are the proton donor-acceptor separation R and the ratio, D1/D2, between the proton affinity of a donor with one and two protons. Depending on the values of these two parameters the model describes four qualitatively different ground state potential energy surfaces, having zero, one, two, or four saddle points. Only for the latter are there four stable tautomers. In the limit D2 = D1 the model reduces to two decoupled hydrogen bonds. As R decreases a transition can occur from a synchronous concerted to an asynchronous concerted to a sequential mechanism for double proton transfer.

11.
J Chem Phys ; 140(17): 174508, 2014 May 07.
Artículo en Inglés | MEDLINE | ID: mdl-24811647

RESUMEN

This work considers how the properties of hydrogen bonded complexes, X-H⋯Y, are modified by the quantum motion of the shared proton. Using a simple two-diabatic state model Hamiltonian, the analysis of the symmetric case, where the donor (X) and acceptor (Y) have the same proton affinity, is carried out. For quantitative comparisons, a parametrization specific to the O-H⋯O complexes is used. The vibrational energy levels of the one-dimensional ground state adiabatic potential of the model are used to make quantitative comparisons with a vast body of condensed phase data, spanning a donor-acceptor separation (R) range of about 2.4-3.0 Å, i.e., from strong to weak hydrogen bonds. The position of the proton (which determines the X-H bond length) and its longitudinal vibrational frequency, along with the isotope effects in both are described quantitatively. An analysis of the secondary geometric isotope effect, using a simple extension of the two-state model, yields an improved agreement of the predicted variation with R of frequency isotope effects. The role of bending modes is also considered: their quantum effects compete with those of the stretching mode for weak to moderate H-bond strengths. In spite of the economy in the parametrization of the model used, it offers key insights into the defining features of H-bonds, and semi-quantitatively captures several trends.

12.
Phys Rev Lett ; 110(20): 206402, 2013 May 17.
Artículo en Inglés | MEDLINE | ID: mdl-25167433

RESUMEN

Thermodynamic properties of the Hubbard model on the anisotropic triangular lattice at half filling are calculated by the finite-temperature Lanczos method. The charge susceptibility exhibits clear signatures of a Mott metal-insulator transition. The metallic phase is characterized by a small charge susceptibility, large entropy, large renormalized quasiparticle mass, and large spin susceptibility. The fluctuating local magnetic moment in the metallic phase is large and comparable to that in the insulating phase. These bad metallic characteristics occur above a relatively low coherence temperature, as seen in organic charge transfer salts.

13.
J Chem Phys ; 137(16): 164319, 2012 Oct 28.
Artículo en Inglés | MEDLINE | ID: mdl-23126722

RESUMEN

A two-state model Hamiltonian is proposed, which can describe the coupling of twisting displacements to charge-transfer behavior in the ground and excited states of a general monomethine dye molecule. This coupling may be relevant to the molecular mechanism of environment-dependent fluorescence yield enhancement. The model is parameterized against quantum chemical calculations on different protonation states of the green fluorescent protein chromophore, which are chosen to sample different regimes of detuning from the cyanine (resonant) limit. The model provides a simple yet realistic description of the charge transfer character along two possible excited state twisting channels associated with the methine bridge. It describes qualitatively different behavior in three regions that can be classified by their relationship to the resonant (cyanine) limit. The regimes differ by the presence or absence of twist-dependent polarization reversal and the occurrence of conical intersections. We find that selective biasing of one twisting channel over another by an applied diabatic biasing potential can only be achieved in a finite range of parameters near the cyanine limit.

14.
J Chem Phys ; 136(23): 234313, 2012 Jun 21.
Artículo en Inglés | MEDLINE | ID: mdl-22779599

RESUMEN

We analyze the low-energy electronic structure of a series of symmetric cationic diarylmethanes, which are bridge-substituted derivatives of Michler's Hydrol Blue. We use a four-electron, three-orbital complete active space self-consistent field and multi-state multi-reference perturbation theory model to calculate a three-state diabatic effective Hamiltonian for each dye in the series. We exploit an isolobal analogy between the active spaces of the self-consistent field solutions for each dye to represent the electronic structure in a set of analogous diabatic states. The diabatic states can be identified with the bonding structures in classical resonance-theoretic models of cyanine dyes. We identify diabatic states with opposing charge and bond-order localization, analogous to the classical resonance structures, and a third state with charge on the bridge. While the left- and right-charged structures are similar for all dyes, the structure of the bridge-charged diabatic state, and the Hamiltonian matrix elements connected to it, change significantly across the series. The change is correlated with an inversion of the sign of the charge carrier on the bridge, which changes from an electron pair to a hole as the series is traversed.

15.
Proc Natl Acad Sci U S A ; 106(11): 4219-24, 2009 Mar 17.
Artículo en Inglés | MEDLINE | ID: mdl-19251667

RESUMEN

In 1968, Fröhlich showed that a driven set of oscillators can condense with nearly all of the supplied energy activating the vibrational mode of lowest frequency. This is a remarkable property usually compared with Bose-Einstein condensation, superconductivity, lasing, and other unique phenomena involving macroscopic quantum coherence. However, despite intense research, no unambiguous example has been documented. We determine the most likely experimental signatures of Fröhlich condensation and show that they are significant features remote from the extraordinary properties normally envisaged. Fröhlich condensates are classified into 3 types: weak condensates in which profound effects on chemical kinetics are possible, strong condensates in which an extremely large amount of energy is channeled into 1 vibrational mode, and coherent condensates in which this energy is placed in a single quantum state. Coherent condensates are shown to involve extremely large energies, to not be produced by the Wu-Austin dynamical Hamiltonian that provides the simplest depiction of Fröhlich condensates formed using mechanically supplied energy, and to be extremely fragile. They are inaccessible in a biological environment. Hence the Penrose-Hameroff orchestrated objective-reduction model and related theories for cognitive function that embody coherent Fröhlich condensation as an essential element are untenable. Weak condensates, however, may have profound effects on chemical and enzyme kinetics, and may be produced from biochemical energy or from radio frequency, microwave, or terahertz radiation. Pokorný's observed 8.085-MHz microtubulin resonance is identified as a possible candidate, with microwave reactors (green chemistry) and terahertz medicine appearing as other feasible sources.


Asunto(s)
Transferencia de Energía , Modelos Químicos , Vibración , Enzimas/metabolismo , Cinética , Teoría Cuántica , Tubulina (Proteína)/química
16.
J Sci Food Agric ; 92(13): 2672-8, 2012 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-22523006

RESUMEN

BACKGROUND: Crop management tools have been shown to affect barley kernel size and grain protein content, but the direct effect on malt quality is not well understood. The present study investigated the effect of seeding rate, nitrogen fertilisation and cultivar on malt quality. RESULTS: Higher seeding rates produced barley with less grain protein and smaller, more uniformly sized kernels. The small, uniformly sized kernels modified more completely, leading to malt with higher extract and lower wort ß-glucan than malt from low-seeding-rate barley. Increasing rates of nitrogen fertilisation caused grain protein levels to increase, which limited endosperm modification and reduced malt extract levels. AC Metcalfe showed better modification and higher malt extract than CDC Copeland, but CDC Copeland had better protein modification at higher fertilisation rates, which resulted in less reduction of malt extract as nitrogen rate increased. CONCLUSION: Higher seeding rates reduced kernel size and grain protein levels without compromising malt extract owing to better endosperm modification of the more uniformly sized kernels. Negative effects of higher nitrogen rates on malt quality can be reduced through development of cultivars with improved ability to modify protein during malting.


Asunto(s)
Agricultura/métodos , Fertilizantes , Hordeum , Nitrógeno/metabolismo , Proteínas de Plantas/metabolismo , Semillas , beta-Glucanos/metabolismo , Hordeum/anatomía & histología , Hordeum/clasificación , Hordeum/metabolismo , Semillas/anatomía & histología , Semillas/metabolismo , Especificidad de la Especie
17.
Phys Rev Lett ; 107(14): 147001, 2011 Sep 30.
Artículo en Inglés | MEDLINE | ID: mdl-22107229

RESUMEN

We consider a model self-energy consisting of an isotropic Fermi liquid term and a marginal Fermi liquid term which is anisotropic over the Fermi surface, vanishing in the same directions as the superconducting gap and the pseudogap. This model self-energy gives a consistent description of experimental results from angle-dependent magnetoresistance, specific heat, de Haas-van Alphen, and measurements of the quasiparticle dispersion near the Fermi surface from photoemission. In particular, we reconcile the strongly doping-dependent anomalous scattering rate observed in angle-dependent magnetoresistance with the almost doping-independent specific heat.

18.
J Chem Phys ; 134(11): 114520, 2011 Mar 21.
Artículo en Inglés | MEDLINE | ID: mdl-21428645

RESUMEN

We derive structure-property relationships for methine ("Brooker") dyes relating the color of the dye and its symmetric parents to its bond alternation in the ground state and also to the dipole properties associated with its low-lying charge-resonance (or charge-transfer) transition. We calibrate and test these relationships on an array of different protonation states of the green fluorescent protein chromophore motif (an asymmetric halochromic methine dye) and its symmetric parent dyes. The relationships rely on the assumption that the diabatic states that define the Platt model for methine dye color [J. R. Platt, J. Chem. Phys. 25, 80 (1956)] can also be distinguished by their single-double bond alternation and by their charge localization character. These assumptions are independent of the primary constraint that defines the diabatic states in the Platt model--specifically, the Brooker deviation rule for methine dyes [L. G. S. Brooker, Rev. Mod. Phys. 14, 275 (1942)]. Taking these assumptions, we show that the Platt model offers an alternate route to known structure-property relationships between the bond length alternation and the quadratic nonlinear polarizability ß. We show also that the Platt model can be parameterized without the need for synthesis of the symmetric parents of a given dye, using the dipole data obtained through spectroscopic measurements. This suggests that the Platt model parameters may be used as independent variables in free-energy relationships for chromophores whose symmetric parents cannot be synthesized or chromophores strongly bound to biomolecular environments. The latter category includes several recently characterized biomolecular probe constructs. We illustrate these concepts by an analysis of previously reported electroabsorption and second-harmonic generation experiments on green fluorescent proteins.

19.
J Chem Phys ; 135(24): 244110, 2011 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-22225147

RESUMEN

We consider the quantum entanglement of the electronic and vibrational degrees of freedom in molecules with tendencies towards double welled potentials. In these bipartite systems, the von Neumann entropy of the reduced density matrix is used to quantify the electron-vibration entanglement for the lowest two vibronic wavefunctions obtained from a model Hamiltonian based on coupled harmonic diabatic potential-energy surfaces. Significant entanglement is found only in the region in which the ground vibronic state contains a density profile that is bimodal (i.e., contains two separate local maxima). However, in this region two distinct types of density and entanglement profiles are found: one type arises purely from the degeneracy of energy levels in the two potential wells and is destroyed by slight asymmetry, while the other arises through strong interactions between the diabatic levels of each well and is relatively insensitive to asymmetry. These two distinct types are termed fragile degeneracy-induced entanglement and persistent entanglement, respectively. Six classic molecular systems describable by two diabatic states are considered: ammonia, benzene, BNB, pyridine excited triplet states, the Creutz-Taube ion, and the radical cation of the "special pair" of chlorophylls involved in photosynthesis. These chemically diverse systems are all treated using the same general formalism and the nature of the entanglement that they embody is elucidated.


Asunto(s)
Electrones , Teoría Cuántica , Amoníaco/química , Bacterioclorofila A/química , Benceno/química , Simulación por Computador , Modelos Químicos , Piridinas/química , Termodinámica
20.
Front Cell Infect Microbiol ; 11: 759697, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-35004344

RESUMEN

The cervicovaginal microbiome plays an important role in protecting women from dysbiosis and infection caused by pathogenic microorganisms. In healthy reproductive-age women the cervicovaginal microbiome is predominantly colonized by protective Lactobacillus spp. The loss of these protective bacteria leads to colonization of the cervicovaginal microenvironment by pathogenic microorganisms resulting in dysbiosis and bacterial vaginosis (BV). Mobiluncus mulieris and Eggerthella sp. are two of the many anaerobes that can contribute to BV, a condition associated with multiple adverse obstetric and gynecological outcomes. M. mulieris has been linked to high Nugent scores (relating to BV morphotypes) and preterm birth (PTB), whilst some bacterial members of the Eggerthellaceae family are highly prevalent in BV, and identified in ~85-95% of cases. The functional impact of M. mulieris and Eggerthella sp. in BV is still poorly understood. To determine the individual immunometabolic contributions of Eggerthella sp. and M. mulieris within the cervicovaginal microenvironment, we utilized our well-characterized human three-dimensional (3-D) cervical epithelial cell model in combination with multiplex immunoassays and global untargeted metabolomics approaches to identify key immune mediators and metabolites related to M. mulieris and Eggerthella sp. infections. We found that infection with M. mulieris significantly elevated multiple proinflammatory markers (IL-6, IL-8, TNF-α and MCP-1) and altered metabolites related to energy metabolism (nicotinamide and succinate) and oxidative stress (cysteinylglycine, cysteinylglycine disulfide and 2-hydroxygluatrate). Eggerthella sp. infection significantly elevated multiple sphingolipids and glycerolipids related to epithelial barrier function, and biogenic amines (putrescine and cadaverine) associated with elevated vaginal pH, vaginal amine odor and vaginal discharge. Our study elucidated that M. mulieris elevated multiple proinflammatory markers relating to PTB and STI acquisition, as well as altered energy metabolism and oxidative stress, whilst Eggerthella sp. upregulated multiple biogenic amines associated with the clinical diagnostic criteria of BV. Future studies are needed to evaluate how these bacteria interact with other BV-associated bacteria within the cervicovaginal microenvironment.


Asunto(s)
Microbiota , Nacimiento Prematuro , Vaginosis Bacteriana , Femenino , Humanos , Recién Nacido , Mobiluncus , Embarazo , Vagina
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