Vibrational polariton transport in disordered media.

Chemical reactions and energy transport phenomena have been experimentally reported to be significantly affected by strong light-matter interactions and vibrational polariton formation. These quasiparticles exhibit nontrivial transport phenomena due to the long-range correlations induced by the photonic system and elastic and inelastic scattering processes driven by matter disorder. In this article, we employ the Ioffe-Regel criterion to obtain vibrational polariton mobility edges and to identify distinct regimes of delocalization and transport under variable experimental conditions of light-matter detuning, disorder, and interaction strength. Correlations between the obtained trends and recent observations of polariton effects on reactivity are discussed, and essential differences between transport phenomena in organic electronic exciton and vibrational polaritons are highlighted. Our transport diagrams show the rich diversity of transport phenomena under vibrational strong coupling and indicate that macroscopic delocalization is favored at negative detuning and large light-matter interaction strength. We also find the surprising feature that, despite the presence of dephasing-induced inelastic scattering processes, macroscopic lower polariton delocalization and wave transport are expected to persist experimentally, even in modes with small photonic weight.

Two-dimensional infrared spectroscopy of vibrational polaritons.

We report experimental 2D infrared (2D IR) spectra of coherent light-matter excitations--molecular vibrational polaritons. The application of advanced 2D IR spectroscopy to vibrational polaritons challenges and advances our understanding in both fields. First, the 2D IR spectra of polaritons differ drastically from free uncoupled excitations and a new interpretation is needed. Second, 2D IR uniquely resolves excitation of hybrid light-matter polaritons and unexpected dark states in a state-selective manner, revealing otherwise hidden interactions between them. Moreover, 2D IR signals highlight the impact of molecular anharmonicities which are applicable to virtually all molecular systems. A quantum-mechanical model is developed which incorporates both nuclear and electrical anharmonicities and provides the basis for interpreting this class of 2D IR spectra. This work lays the foundation for investigating phenomena of nonlinear photonics and chemistry of molecular vibrational polaritons which cannot be probed with traditional linear spectroscopy.

Computational method for highly constrained molecular dynamics of rigid bodies: Coarse-grained simulation of auxetic two-dimensional protein crystals.

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on Molecular Dynamics (MD) that addresses the geometric degrees of freedom of an auxetic two-dimensional protein crystal. This model consists of a network of impenetrable rigid squares linked through massless rigid rods. Our MD methodology extends the well-known protocols SHAKE and RATTLE to include highly non-linear holonomic and non-holonomic constraints, with an emphasis on collision detection and response between anisotropic rigid bodies. The presented method enables the simulation of long-time dynamics with reasonably large time steps. The data extracted from the simulations allow the characterization of the dynamical correlations featured by the protein subunits, which show a persistent motional interdependence across the array. On the other hand, non-holonomic constraints (collisions between subunits) increase the number of inhomogeneous deformations of the network, thus driving it away from an isotropic response. Our work provides the first long-timescale simulation of the dynamics of protein crystals and offers insights into promising mechanical properties afforded by these materials.

State-Selective Polariton to Dark State Relaxation Dynamics.

The modification of vibrational dynamics is essential for controlling chemical reactions and IR photonic applications. The hybridization between cavity modes and molecular vibrational modes provides a new way to control molecular dynamics. In this work, we study the dynamics of molecular vibrational polaritons in various solvent environments. We find the dynamics of the polariton system is strongly influenced by the nature of the solvents. While the relaxation from upper polariton (UP) to dark modes is always fast (<5 ps) regardless of the medium, lower polariton (LP) in low polarity solvents shows much slower transfer (10-30 ps) into dark modes, despite the fact that the LP lifetime remains within 5 ps. This result suggests that in the latter media, the energy pumped into the LP is first transferred into intermediate states which only subsequently decay into dark modes. In contrast, in solvent environments that strongly interact with the solute, the LP population relaxes into the dense dark state manifold within a much faster time scale. We propose the intermediate state to be the high-lying excited states of dark modes, which are effectively populated by LP via, e.g., ladder-climbing. Such population in the high-lying states can be retained for tens of picoseconds, which could be pertinent to recently observed cavity-modified chemistry.

Deriving uniform semiclassical approximations for one-dimensional fermionic systems.

A complete derivation is provided of the uniform semiclassical approximations to the particle and kinetic energy densities of N noninteracting bounded fermions in one dimension. The employed methodology allows the inclusion of non-perturbative quantum effects, including tunneling and quantum oscillations, via an infinite resummation of the Poisson summation formula. We explore the analytic behavior, physical meaning, and the relationship between the semiclassical uniform approximations for the fermionic kinetic energy and particle densities.

Morphological and molecular confirmation of Myxobolus cerebralis myxospores infecting wild­caught and cultured trout in North Carolina (SE USA).

We used microscopy and molecular biology to provide the first documentation of infections of Myxobolus cerebralis (Myxozoa: Myxobolidae), the etiological agent of whirling disease, in trout (Salmonidae) from North Carolina (USA) river basins. A total of 1085 rainbow trout Oncorhynchus mykiss, 696 brown trout Salmo trutta, and 319 brook trout Salvelinus fontinalis from 43 localities across 9 river basins were screened. Myxospores were observed microscopically in pepsin-trypsin digested heads of rainbow and brown trout from the Watauga River Basin. Those infections were confirmed using the prescribed nested polymerase chain reaction (PCR; 18S rDNA), which also detected infections in rainbow, brown, and brook trout from the French Broad River Basin and the Yadkin Pee-Dee River Basin. Myxospores were 9.0-10.0 µm (mean ± SD = 9.6 ± 0.4; N = 119) long, 8.0-10.0 µm (8.8 ± 0.6; 104) wide, and 6.0-7.5 µm (6.9 ± 0.5; 15) thick and had polar capsules 4.0-6.0 µm (5.0 ± 0.5; 104) long, 2.5-3.5 µm (3.1 ± 0.3; 104) wide, and with 5 or 6 polar filament coils. Myxospores from these hosts and rivers were morphologically indistinguishable and molecularly identical, indicating conspecificity, and the resulting 18S rDNA and ITS-1 sequences derived from these myxospores were 99.5-100% and 99.3-99.8% similar, respectively, to published GenBank sequences ascribed to M. cerebralis. This report comprises the first taxonomic circumscription and molecular confirmation of M. cerebralis in the southeastern USA south of Virginia.

Is Marine Dispersion of the Lethargic Crab Disease Possible? Assessing the Tolerance of Exophiala cancerae to a Broad Combination of Salinities, Temperatures, and Exposure Times.

Since 1997, an emergent fungal disease named lethargic crab disease (LCD) has decimated stocks of the edible mangrove land crab Ucides cordatus (Linnaeus, 1763) (Brachyura: Ocypodidae) along the Brazilian coast, threatening the mangrove ecosystem and causing socioeconomic impacts. Evidence from a variety of sources suggests that the black yeast Exophiala cancerae (Herpotrichiellaceae, Chaetothyriales) has been responsible for such epizootic events. Based on the spatiotemporal patterns of the LCD outbreaks, the well-established surface ocean currents, and the range of ecological traits of Exophiala spp., a marine dispersal hypothesis may be proposed. Using in vitro experiments, we tested the survival and growth of E. cancerae CBS 120420 in a broad combination of salinities, temperatures, and exposure times. While variation in salinity did not significantly affect the growth of colony-forming units (CFUs) (P > 0.05), long exposure times visibly influenced an increase in CFUs growth (P < 0.05). However, higher temperature (30 °C) caused a reduction of about 1.2-fold in CFUs growth (P < 0.05). This result suggests that sea surface temperatures either above or below the optimum growth range of E. cancerae could play a key role in the apparent north-south limits in the geographical distribution of LCD outbreaks. In light of our results, we conclude that a fundamental step toward the understanding of LCD epidemiological dynamics should comprise a systematic screening of E. cancerae in estuarine and coastal waters.

A new species of Spirorchis MacCallum, 1918 (Digenea: Schistosomatoidea) and Spirorchis cf. scripta from chicken turtle, Deirochelys reticularia (Emydidae), with an emendation and molecular phylogeny of Spirorchis.

Chicken turtles, Deirochelys reticularia (Latreille in Sonnini et Latreille) (Testudines: Emydidae) from Alabama, USA were infected by Spirorchis collinsi Roberts et Bullard sp. n. and Spirorchis cf. scripta. The new species is most easily differentiated from its congeners by the combination of having caeca that extend far beyond the genitalia, intercaecal genitalia positioned in the middle portion of the body, a testicular column that nearly abuts the caecal bifurcation, a cirrus sac positioned between the testes and ovary, a massive Mehlis' gland, an elongate, longitudinal metraterm that extends anteriad beyond the level of the ovary, a pre-ovarian genital pore, and a prominent, intercaecal Manter's organ. The specimens of S. cf. scripta differed from the holotype and published descriptions of Spirorchis scripta Stunkard, 1923 by several subtle morphological features, perhaps comprising intraspecific variation, but collectively warranted a detailed description herein. Based on examinations of the aforementioned specimens plus the holotype, paratypes and vouchers of morphologically-similar congeners, Spirorchis MacCallum, 1918 is emended to include the presence of oral sucker spines, a pharynx, lateral oesophageal diverticula ('plicate organ') and a median oesophageal diverticulum ('oeseophageal pouch'). Phylogenetic analysis of the nuclear large subunit rDNA (28S) recovered S. collinsi sister to Spirorchis picta Stunkard, 1923, > 99% similarity between S. cf. scripta and S. scripta, and a monophyletic Spirorchis MacCallum, 1918. No blood fluke infection has been reported previously from these drainages, Alabama, or this turtle species. This is the first new species of Spirorchis to be described from North America in 26 years.

Blood flukes of Asiatic softshell turtles: revision of Coeuritrema Mehra, 1933 (Digenea: Schistosomatoidea) and a new species infecting Chinese softshell turtles, Pelodiscus sinensis (Trionychidae), from Vietnam.

Coeuritrema Mehra, 1933, previously regarded as a junior subjective synonym of Hapalorhynchus Stunkard, 1922, herein is revised to include Coeuritrema lyssimus Mehra, 1933 (type species), Coeuritrema rugatus (Brooks et Sullivan, 1981) comb. n., and Coeuritrema platti Roberts et Bullard sp. n. These genera are morphologically similar by having a ventral sucker, non-fused caeca, two testes, a pre-testicular cirrus sac, an intertesticular ovary, and a common genital pore that opens dorsally and in the sinistral half of the body. Phylogenetic analysis of the D1-D3 domains of the nuclear large subunit ribosomal DNA (28S) suggested that Coeuritrema and Hapalorhynchus share a recent common ancestor. Coeuritrema is morphologically most easily differentiated from Hapalorhynchus by having ventrolateral tegumental papillae and a definitive metraterm that is approximately 3-7× longer than the uterus. Coeuritrema comprises species that reportedly infect Asiatic softshell turtles (Testudines: Trionychidae) only, whereas Hapalorhynchus (as currently defined) comprises blood flukes that reportedly infect those hosts plus North American musk turtles (Sternotherus Bell in Gray) and mud turtles (Kinosternon Spix), both Kinosternidae, North American snapping turtles (Chelydridae), Asiatic hard-shelled turtles (Geoemydidae) and African pleurodirans (Pelomedusidae). Coeuritrema platti sp. n. infects the blood of Chinese softshell turtles, Pelodiscus sinensis (Wiegmann), cultured in the Da Rang River Basin (Phu Yen Province, Vietnam). It differs from C. lyssimus by having a narrow hindbody (< 1.6× forebody width), ventrolateral tegumental papillae restricted to the hindbody, a short cirrus sac (< 10% of corresponding body length), a transverse ovary buttressing the caeca, a short, wholly pre-ovarian metraterm (~ 10% of corresponding body length), and a submarginal genital pore. It differs from C. rugatus by having small ventrolateral tegumental papillae, testes without deep lobes, and a Laurer's canal pore that opens posterior to the vitelline reservoir and dorsal to the oviducal seminal receptacle. The new species is only the second turtle blood fluke reported from Vietnam.

Corrections to Thomas-Fermi densities at turning points and beyond.

Uniform semiclassical approximations for the number and kinetic-energy densities are derived for many noninteracting fermions in one-dimensional potentials with two turning points. The resulting simple, closed-form expressions contain the leading corrections to Thomas-Fermi theory, involve neither sums nor derivatives, are spatially uniform approximations, and are exceedingly accurate.

Blood flukes (Digenea: Aporocotylidae) infecting body cavity of South American catfishes (Siluriformes: Pimelodidae): two new species from rivers in Bolivia, Guyana and Peru with a re-assessment of Plehniella Szidat, 1951.

Plehniella Szidat, 1951 is emended based on new collections from South American long-whiskered catfishes. It is clearly differentiated from Sanguinicola Plehn, 1905 by lacking lateral tegumental body spines and by having 6 asymmetrical caeca. Plehniella sabajperezi sp. n. infects body cavity of Pimelodus albofasciatus (Mees) from the Demerara and Rupununi Rivers (Guyana) and Pimelodus blochii (Valenciennes) from Lake Tumi Chucua (Bolivia) and Napo River (Peru). It differs from Plehniella coelomicola Szidat, 1951 (type species) by having a thin-walled vas deferens that greatly exceeds the length of cirrus-sac and that joins the cirrus-sac at level of ovovitelline duct and ootype, an internal seminal vesicle that is absent or diminutive, and a cirrus-sac that is spheroid, nearly marginal, and envelops the laterally-directed distal portion of the male genitalia. Plehniella armbrusteri sp. n. infects body cavity of P. blochii from Lake Tumi Chucua (Bolivia). It differs from P. coelomicola and P. sabajperezi by having a relatively ovoid body, a massive intestine comprising caeca that are deeply-lobed to diverticulate and terminate in the posterior half of the body, a testis that flanks the distal tips of the posteriorly-directed caeca, and a proximal portion of the vas deferens that loops ventral to the testis. Small adults (Plehniella sp.) collected from body cavity of Pimelodus grosskopfii (Steindachner) from Cienega de Jobo and Canal del Dique (Colombia) differ from congeners by having a posteriorly-constricted body region, an anterior sucker with concentric rows of minute spines, an elongate anterior oesophageal swelling, short and wide caeca, and a male genital pore that opens proportionally more anteriad. This study nearly doubles the number of aporocotylids documented from South America Rivers and comprises the first record of a fish blood fluke from P. blochii, P. albofasciatus and P. grosskopfii as well as from Bolivia, Colombia, Guyana or Peru.

Theoretical formulation of chemical equilibrium under vibrational strong coupling.

Experiments have suggested that strong interactions between molecular ensembles and infrared microcavities can be employed to control chemical equilibria. Nevertheless, the primary mechanism and key features of the effect remain largely unexplored. In this work, we develop a theory of chemical equilibrium in optical microcavities, which allows us to relate the equilibrium composition of a mixture in different electromagnetic environments. Our theory shows that in planar microcavities under strong coupling with polyatomic molecules, hybrid modes formed between all dipole-active vibrations and cavity resonances contribute to polariton-assisted chemical equilibrium shifts. To illustrate key aspects of our formalism, we explore a model SN2 reaction within a single-mode infrared resonator. Our findings reveal that chemical equilibria can be shifted towards either direction of a chemical reaction, depending on the oscillator strength and frequencies of reactant and product normal modes. Polariton-induced zero-point energy changes provide the dominant contributions, though the effects in idealized single-mode cavities tend to diminish quickly as the temperature and number of molecules increase. Our approach is valid in generic electromagnetic environments and paves the way for understanding and controlling chemical equilibria with microcavities.

Black yeast biota in the mangrove, in search of the origin of the lethargic crab disease (LCD).

Knowledge of natural ecology is essential for a better understanding of pathogenicity and opportunism in black yeast-like fungi. Although etiological agents of diseases caused by these fungi are supposed to originate from the environment, their isolation from nature is difficult. This is probably due to their oligotrophic nature, low competitive ability, and, overall, insufficient data on their natural habitat. We obtained environmental samples from mangrove areas where mortalities by lethargic crab disease (LCD) are reported and areas without disease recorded. Isolation of chaetothyrialean black yeasts and relatives was performed using a highly selective protocol. Species-specific primers were used to determine if these isolates represented Exophiala cancerae or Fonsecaea brasiliensis, two proven agents of LCD, in order to test hypotheses about the origin of the disease. Isolates, identified by morphology as Fonsecaea- or Exophiala-like, were tested specific diagnostic markers for the fungi associated with LCD. Although several black fungi were isolated, the main causative agent of the LCD, E. cancerae, was not found. Molecular markers for F. brasiliensis revealed 10 positive bands for isolates from biofilms on mangrove leaves, branches, and aerial roots, of which four were confirmed by ITS sequencing. The absence of E. cancerae in environmental samples suggests that the species is dependent on the crab, as a genuine pathogen, different from F. brasiliensis, which is probably not dependent on the host species, U. cordatus. However, we did not attempt isolation from the marine water, which may represent the pathway of dispersion of the black yeast species between neighbor mangroves.

Theoretical Analysis of Exciton Wave Packet Dynamics in Polaritonic Wires.

We present a comprehensive study of the exciton wave packet evolution in disordered lossless polaritonic wires. Our simulations reveal signatures of ballistic, diffusive, and subdiffusive exciton dynamics under strong light-matter coupling and identify the typical time scales associated with the transitions between these qualitatively distinct transport phenomena. We determine optimal truncations of the matter and radiation subsystems required for generating reliable time-dependent data from computational simulations at an affordable cost. The time evolution of the photonic part of the wave function reveals that many cavity modes contribute to the dynamics in a nontrivial fashion. Hence, a sizable number of photon modes is needed to describe exciton propagation with a reasonable accuracy. We find and discuss an intriguingly common lack of dominance of the photon mode on resonance with matter in both the presence and absence of disorder. We discuss the implications of our investigations for the development of theoretical models and analysis of experiments where coherent intermolecular energy transport and static disorder play an important role.

Multimode polariton effects on molecular energy transport and spectral fluctuations.

Despite the potential paradigm breaking capability of microcavities to control chemical processes, the extent to which photonic devices change properties of molecular materials is still unclear, in part due to challenges in modeling hybrid light-matter excitations delocalized over many length scales. We overcome these challenges for a photonic wire under strong coupling with a molecular ensemble. Our simulations provide a detailed picture of the effect of photonic wires on spectral and transport properties of a disordered molecular material. We find stronger changes to the probed molecular observables when the cavity is redshifted relative to the molecules and energetic disorder is weak. These trends are expected to hold also in higher-dimensional cavities, but are not captured with theories that only include a single cavity-mode. Therefore, our results raise important issues for future experiments and model building focused on unraveling new ways to manipulate chemistry with optical cavities.

The solvation, partitioning, hydrogen bonding, and dimerization of nucleotide bases: a multifaceted challenge for quantum chemistry.

We present M06-2X density functional calculations of the chloroform/water partition coefficients of cytosine, thymine, uracil, adenine, and guanine and calculations of the free energies of association of selected unsubstituted and alkylated nucleotide base pairs in chloroform and water. Both hydrogen bonding and π-π stacking interactions are considered. Solvation effects are treated using the continuum solvent models SM8, SM8AD, and SMD, including geometry optimization in solution. Comparison of theoretical results with available experimental data indicates that all three of these solvation models predict the chloroform-water partition coefficients for the studied nucleobases qualitatively well, with mean unsigned errors in the range of 0.4-1.3 log units. All three models correctly predict the preference for hydrogen bonding over stacking for nucleobase pairs solvated in chloroform, and SM8, SM8AD, and SMD show similar accuracy in predicting the corresponding free energies of association. The agreement between theory and experiment for the association free energies of the dimers in water is more difficult to assess, as the relevant experimental data are indirect. Theory predicts that the stacking interaction of nucleobases in water is more favorable than hydrogen bonding for only two out of three tested hetero-dimers.

Fulfilling Koch's postulates confirms the mycotic origin of Lethargic Crab Disease.

In the northeast region of the Brazilian coast, a disease has been causing massive mortalities of populations of the mangrove land crab, Ucides cordatus (L.) since 1997. The clinical signs of this disease, which include lethargy and ataxia, led to the disease being termed Lethargic Crab Disease (LCD). Evidence from a variety of sources indicates that there is an association between LCD and a new species of black yeast, Exophiala cancerae de Hoog, Vicente, Najafzadeh, Badali, Seyedmousavi & Boeger. This study tests this putative correlation through in vivo experiments. Disease-free specimens of U. cordatus were experimentally infected with Exophiala cancerae (strain CBS 120420) isolate. During the 30-day experimental period, only a single death was observed within the control crabs. However, at the end of this period, crabs that were inoculated once or three-times with mycelial elements and hyphae of E. cancerae had a 60% and 50% mortality rates, respectively (n = 6 and n = 5). These results support that the fungal agent is pathogenic and is the causative agent of LCD. Species-specific molecular markers confirm the presence of E. cancerae (strain CBS 120420) in recovered colonies and tissue samples from the infected animals. The experimentally infected crabs manifested signs (lethargy, ataxia and tetany) that were consistent to LCD-affected animals in the environment. These results fulfil Koch's postulates and the hypothesis that the tested strain of Exophiala cancerae is a causative agent of LCD is accepted.

Specific primers for the detection of the black-yeast fungus associated with lethargic crab disease (LCD).

Lethargic crab disease (LCD) is an emerging infirmity that has been causing extensive mortalities in populations of the mangrove land crab Ucides cordatus (Ocypodidae) along the Atlantic coast of Brazil. Previous studies have indicated that LCD is associated with a dematiaceous fungus, Exophiala cancerae de Hoog et al. In the present study, we sequenced the internal transcribed spacer (ITS) of the rDNA region of this black yeast species and developed species-specific PCR primers. Sensitivity tests indicated that the developed protocol is capable of detecting very small amounts of target DNA. Also, the application of the protocol to a variety of other dematiaceous fungi did not generate any false positives. The specific primers provided in the present study represent an important tool for rapidly surveying a large number of crab individuals, as well as environmental samples. Such knowledge will be instrumental in understanding the epidemiological dynamics of LCD.

Hypoplasia of C1's posterior arch: Is there an ideal anatomical classification?

BACKGROUND: Congenital anomalies of the atlas are rare and usually occur in conjunction with other congenital variants. They include a wide spectrum of anomalies ranging from clefts to hypoplasia or aplasia of its arches that may contribute to spinal cord compressive syndrome. CASE DESCRIPTION: A 54-year-old male presented with the sudden onset of a severe quadriparesis and loss of proprioception after a minor fall. The magnetic resonance (MR) scan showed cord compression at the C1 level attributed to C1 arch hypoplasia. Two months following a decompressive C1 laminectomy without fusion, and the patient was symptom free. CONCLUSION: Posterior C1 arch hypoplasia is a rare anomaly that can contribute to cervical cord compression and myelopathy. The optimal surgical management may include, as in this case, a posterior decompression without fusion.

Prediction of SAMPL2 aqueous solvation free energies and tautomeric ratios using the SM8, SM8AD, and SMD solvation models.

We applied the solvation models SM8, SM8AD, and SMD in combination with the Minnesota M06-2X density functional to predict vacuum-water transfer free energies (Task 1) and tautomeric ratios in aqueous solution (Task 2) for the SAMPL2 test set. The bulk-electrostatic contribution to the free energy of solvation is treated as follows: SM8 employs the generalized Born model with the Coulomb field approximation, SM8AD employs the generalized Born approximation with asymmetric descreening, and SMD solves the nonhomogeneous Poisson equation. The non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell is treated as a sum of terms that are products of geometry-dependent atomic surface tensions and solvent-accessible surface areas of the individual atoms of the solute. On average, three models tested in the present work perform similarly. In particular, we achieved mean unsigned errors of 1.3 (SM8), 2.0 (SM8AD), and 2.6 kcal/mol (SMD) for the aqueous free energies of 30 out of 31 compounds with known reference data involved in Task 1 and mean unsigned errors of 2.7 (SM8), 1.8 (SM8AD), and 2.4 kcal/mol (SMD) in the free energy differences (tautomeric ratios) for 21 tautomeric pairs in aqueous solution involved in Task 2.