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.

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.

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.

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.

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.

Intermolecular vibrational energy transfer enabled by microcavity strong light-matter coupling.

Selective vibrational energy transfer between molecules in the liquid phase, a difficult process hampered by weak intermolecular forces, is achieved through polaritons formed by strong coupling between cavity photon modes and donor and acceptor molecules. Using pump-probe and two-dimensional infrared spectroscopy, we found that the excitation of the upper polariton, which is composed mostly of donors, can efficiently relax to the acceptors within ~5 picoseconds. The energy-transfer efficiency can be further enhanced by increasing the cavity lifetime, suggesting that the energy transfer is a polaritonic process. This vibrational energy-transfer pathway opens doors for applications in remote chemistry, sensing mechanisms, and vibrational polariton condensation.

Correction: Polariton chemistry: controlling molecular dynamics with optical cavities.

[This corrects the article DOI: 10.1039/C8SC01043A.].

International Legal Approaches to Neurosurgery for Psychiatric Disorders.

Neurosurgery for psychiatric disorders (NPD), also sometimes referred to as psychosurgery, is rapidly evolving, with new techniques and indications being investigated actively. Many within the field have suggested that some form of guidelines or regulations are needed to help ensure that a promising field develops safely. Multiple countries have enacted specific laws regulating NPD. This article reviews NPD-specific laws drawn from North and South America, Asia and Europe, in order to identify the typical form and contents of these laws and to set the groundwork for the design of an optimal regulation for the field. Key challenges for this design that are revealed by the review are how to define the scope of the law (what should be regulated), what types of regulations are required (eligibility criteria, approval procedures, data collection, and oversight mechanisms), and how to approach international harmonization given the potential migration of researchers and patients.

Manipulating optical nonlinearities of molecular polaritons by delocalization.

Optical nonlinearities are key resources in the contemporary photonics toolbox, relevant to quantum gate operations and all-optical switches. Chemical modification is often used to control the nonlinear response of materials at the microscopic level, but on-the-fly manipulation of such response is challenging. Tunability of optical nonlinearities in the mid-infrared (IR) is even less developed, hindering its applications in chemical sensing or IR photonic circuitry. Here, we report control of vibrational polariton coherent nonlinearities by manipulation of macroscopic parameters such as cavity longitudinal length or molecular concentration. Further two-dimensional IR investigations reveal that nonlinear dephasing provides the dominant source of the observed ultrafast polariton nonlinearities. The reported phenomena originate from the nonlinear macroscopic polarization stemming from strong coupling between microscopic molecular excitations and a macroscopic photonic cavity mode.

Resonant catalysis of thermally activated chemical reactions with vibrational polaritons.

Interaction between light and matter results in new quantum states whose energetics can modify chemical kinetics. In the regime of ensemble vibrational strong coupling (VSC), a macroscopic number [Formula: see text] of molecular transitions couple to each resonant cavity mode, yielding two hybrid light-matter (polariton) modes and a reservoir of [Formula: see text] dark states whose chemical dynamics are essentially those of the bare molecules. This fact is seemingly in opposition to the recently reported modification of thermally activated ground electronic state reactions under VSC. Here we provide a VSC Marcus-Levich-Jortner electron transfer model that potentially addresses this paradox: although entropy favors the transit through dark-state channels, the chemical kinetics can be dictated by a few polaritonic channels with smaller activation energies. The effects of catalytic VSC are maximal at light-matter resonance, in agreement with experimental observations.

Weighted Gene Co-Expression Analyses Point to Long Non-Coding RNA Hub Genes at Different Schistosoma mansoni Life-Cycle Stages.

Long non-coding RNAs (lncRNAs) (>200 nt) are expressed at levels lower than those of the protein-coding mRNAs, and in all eukaryotic model species where they have been characterized, they are transcribed from thousands of different genomic loci. In humans, some four dozen lncRNAs have been studied in detail, and they have been shown to play important roles in transcriptional regulation, acting in conjunction with transcription factors and epigenetic marks to modulate the tissue-type specific programs of transcriptional gene activation and repression. In Schistosoma mansoni, around 10,000 lncRNAs have been identified in previous works. However, the limited number of RNA-sequencing (RNA-seq) libraries that had been previously assessed, together with the use of old and incomplete versions of the S. mansoni genome and protein-coding transcriptome annotations, have hampered the identification of all lncRNAs expressed in the parasite. Here we have used 633 publicly available S. mansoni RNA-seq libraries from whole worms at different stages (n = 121), from isolated tissues (n = 24), from cell-populations (n = 81), and from single-cells (n = 407). We have assembled a set of 16,583 lncRNA transcripts originated from 10,024 genes, of which 11,022 are novel S. mansoni lncRNA transcripts, whereas the remaining 5,561 transcripts comprise 120 lncRNAs that are identical to and 5,441 lncRNAs that have gene overlap with S. mansoni lncRNAs already reported in previous works. Most importantly, our more stringent assembly and filtering pipeline has identified and removed a set of 4,293 lncRNA transcripts from previous publications that were in fact derived from partially processed mRNAs with intron retention. We have used weighted gene co-expression network analyses and identified 15 different gene co-expression modules. Each parasite life-cycle stage has at least one highly correlated gene co-expression module, and each module is comprised of hundreds to thousands lncRNAs and mRNAs having correlated co-expression patterns at different stages. Inspection of the top most highly connected genes within the modules' networks has shown that different lncRNAs are hub genes at different life-cycle stages, being among the most promising candidate lncRNAs to be further explored for functional characterization.

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.

Correction: Theory for polariton-assisted remote energy transfer.

[This corrects the article DOI: 10.1039/C8SC00171E.].

Weighted gene co-expression analyses point to long non-coding RNA hub genes at different Schistosoma mansoni life-cycle stages

Long non-coding RNAs (lncRNAs) (>200 nt) are expressed at levels lower than those of the protein-coding mRNAs, and in all eukaryotic model species where they have been characterized, they are transcribed from thousands of different genomic loci. In humans, some four dozen lncRNAs have been studied in detail, and they have been shown to play important roles in transcriptional regulation, acting in conjunction with transcription factors and epigenetic marks to modulate the tissue-type specific programs of transcriptional gene activation and repression. In Schistosoma mansoni, around 10,000 lncRNAs have been identified in previous works. However, the limited number of RNA-sequencing (RNA-seq) libraries that had been previously assessed, together with the use of old and incomplete versions of the S. mansoni genome and protein-coding transcriptome annotations, have hampered the identification of all lncRNAs expressed in the parasite. Here we have used 633 publicly available S. mansoni RNA-seq libraries from whole worms at different stages (n = 121), from isolated tissues (n = 24), from cell-populations (n = 81), and from single-cells (n = 407). We have assembled a set of 16,583 lncRNA transcripts originated from 10,024 genes, of which 11,022 are novel S. mansoni lncRNA transcripts, whereas the remaining 5,561 transcripts comprise 120 lncRNAs that are identical to and 5,441 lncRNAs that have gene overlap with S. mansoni lncRNAs already reported in previous works. Most importantly, our more stringent assembly and filtering pipeline has identified and removed a set of 4,293 lncRNA transcripts from previous publications that were in fact derived from partially processed mRNAs with intron retention. We have used weighted gene co-expression network analyses and identified 15 different gene co-expression modules. Each parasite life-cycle stage has at least one highly correlated gene co-expression module, and each module is comprised of hundreds to thousands lncRNAs and mRNAs having correlated co-expression patterns at different stages. Inspection of the top most highly connected genes within the modules’ networks has shown that different lncRNAs are hub genes at different life-cycle stages, being among the most promising candidate lncRNAs to be further explored for functional characterization.

Weighted gene co-expression analyses point to long non-coding RNA hub genes at different Schistosoma mansoni life-cycle stages

Long non-coding RNAs (lncRNAs) (>200 nt) are expressed at levels lower than those of the protein-coding mRNAs, and in all eukaryotic model species where they have been characterized, they are transcribed from thousands of different genomic loci. In humans, some four dozen lncRNAs have been studied in detail, and they have been shown to play important roles in transcriptional regulation, acting in conjunction with transcription factors and epigenetic marks to modulate the tissue-type specific programs of transcriptional gene activation and repression. In Schistosoma mansoni, around 10,000 lncRNAs have been identified in previous works. However, the limited number of RNA-sequencing (RNA-seq) libraries that had been previously assessed, together with the use of old and incomplete versions of the S. mansoni genome and protein-coding transcriptome annotations, have hampered the identification of all lncRNAs expressed in the parasite. Here we have used 633 publicly available S. mansoni RNA-seq libraries from whole worms at different stages (n = 121), from isolated tissues (n = 24), from cell-populations (n = 81), and from single-cells (n = 407). We have assembled a set of 16,583 lncRNA transcripts originated from 10,024 genes, of which 11,022 are novel S. mansoni lncRNA transcripts, whereas the remaining 5,561 transcripts comprise 120 lncRNAs that are identical to and 5,441 lncRNAs that have gene overlap with S. mansoni lncRNAs already reported in previous works. Most importantly, our more stringent assembly and filtering pipeline has identified and removed a set of 4,293 lncRNA transcripts from previous publications that were in fact derived from partially processed mRNAs with intron retention. We have used weighted gene co-expression network analyses and identified 15 different gene co-expression modules. Each parasite life-cycle stage has at least one highly correlated gene co-expression module, and each module is comprised of hundreds to thousands lncRNAs and mRNAs having correlated co-expression patterns at different stages. Inspection of the top most highly connected genes within the modules’ networks has shown that different lncRNAs are hub genes at different life-cycle stages, being among the most promising candidate lncRNAs to be further explored for functional characterization.

Polariton chemistry: controlling molecular dynamics with optical cavities.

Molecular polaritons are the optical excitations which emerge when molecular transitions interact strongly with confined electromagnetic fields. Increasing interest in the hybrid molecular-photonic materials that host these excitations stems from recent observations of their novel and tunable chemistry. Some of the remarkable functionalities exhibited by polaritons include the ability to induce long-range excitation energy transfer, enhance charge conductivity, and inhibit or accelerate chemical reactions. In this review, we explain the effective theories of molecular polaritons which form a basis for the interpretation and guidance of experiments at the strong coupling limit. The theoretical discussion is illustrated with the analysis of innovative applications of strongly coupled molecular-photonic systems to chemical phenomena of fundamental importance to future technologies.

Theory for polariton-assisted remote energy transfer.

Strong-coupling between light and matter produces hybridized states (polaritons) whose delocalization and electromagnetic character allow for novel modifications in spectroscopy and chemical reactivity of molecular systems. Recent experiments have demonstrated remarkable distance-independent long-range energy transfer between molecules strongly coupled to optical microcavity modes. To shed light on the mechanism of this phenomenon, we present the first comprehensive theory of polariton-assisted remote energy transfer (PARET) based on strong-coupling of donor and/or acceptor chromophores to surface plasmons. Application of our theory demonstrates that PARET up to a micron is indeed possible. In particular, we report two regimes for PARET: in one case, strong-coupling to a single type of chromophore leads to transfer mediated largely by surface plasmons while in the other case, strong-coupling to both types of chromophores creates energy transfer pathways mediated by vibrational relaxation. Importantly, we highlight conditions under which coherence enhances or deteriorates these processes. For instance, while exclusive strong-coupling to donors can enhance transfer to acceptors, the reverse turns out not to be true. However, strong-coupling to acceptors can shift energy levels in a way that transfer from acceptors to donors can occur, thus yielding a chromophore role-reversal or "carnival effect". This theoretical study demonstrates the potential for confined electromagnetic fields to control and mediate PARET, thus opening doors to the design of remote mesoscale interactions between molecular systems.

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.

Theory for Nonlinear Spectroscopy of Vibrational Polaritons.

Molecular polaritons have gained considerable attention due to their potential to control nanoscale molecular processes by harnessing electromagnetic coherence. Although recent experiments with liquid-phase vibrational polaritons have shown great promise for exploiting these effects, significant challenges remain in interpreting their spectroscopic signatures. We develop a quantum-mechanical theory of pump-probe spectroscopy for this class of polaritons based on the quantum Langevin equation and the input-output theory. Comparison with recent experimental data shows good agreement upon consideration of the various vibrational anharmonicities that modulate the signals. Finally, a simple and intuitive interpretation of the data based on an effective mode-coupling theory is provided. Our work provides a solid theoretical framework to elucidate nonlinear optical properties of molecular polaritons as well as to analyze further multidimensional spectroscopy experiments on these systems.