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Jonathan Phillips

Publications and source records attributed to Jonathan Phillips.

16 recordsLinked to original sources
arXiv2026

Distinct Structural Dynamics of the Semiquinone State Define a Signalling Pathway in Avian Cryptochrome

The light-dependent magnetic compass of night-migratory songbirds is widely hypothesized to rely on the radical pair mechanism within retinal cryptochrome. However, bridging the mechanistic gap between microsecond quantum spin dynamics and the long-lived, global protein conformational changes required for cellular signalling remains a formidable challenge. Here, we apply redox state-resolved hydrogen/deuterium-exchange mass spectrometry (HDX-MS) to map the conformational landscape of European robin cryptochrome 4a (ErCry4a) across its photocycle. We reveal that photochemical reduction drives robust, allosteric structural transitions across key functional nodes, including the phosphate-binding loop (PBL), protrusion loop (PL), FAD-proximal helix {\alpha}17, and the C-terminal {\alpha}22/{\alpha}23 network. Crucially, we isolate the structural fingerprint of the transient semiquinone, the presumed signalling species. Rather than acting as a linear structural stepping-stone, the semiquinone exhibits a distinct, non-monotonic conformational signature characterized by a transient destabilization of the PBL and PL, contrasting sharply with the global rigidification observed in the fully reduced state. These findings establish the semiquinone as a structurally unique and functionally competent biological entity. Our results provide direct biophysical evidence for a dedicated, high-fidelity structural signalling cascade, detailing how localized quantum-level photochemistry is translated into the precise conformational dynamics required for animal navigation.

physics.bio-ph↗
arXiv2024

Half-kilowatt high energy third harmonic conversion to 50 J @ 10 Hz at 343 nm

We report on frequency tripling of high energy, high repetition rate ns pulses from a cryogenically gas cooled multi-slab Yb:YAG laser system Bivoj/DiPOLE, using a type-I phase matched LBO crystal for second harmonic generation and type-II phase matched LBO crystal for sum frequency generation. We achieved conversion to 343 nm with stable energy of 50 J at repetition rate of 10 Hz and conversion efficiency of 53%.

physics.optics↗
arXiv2021

Promises and Pitfalls of a New Early Warning System for Gentrification in Buffalo, NY

Gentrification and its resultant displacement are one of the many "wicked problems" of social policy. The study of gentrification and displacement spans half a century, concerns a variety of spatial, temporal, and social contexts, and describes socio-political processes of across the globe and throughout history. One current iteration of this field of inquiry are efforts to identify "early indicators" of gentrification and/or displacement, or the creation of "early warning systems" (EWS). The current work adds to scholarship on the utility of developing an EWS by examining the methodological considerations required for such systems to serve a justice-oriented preventative role.

cs.SI↗
arXiv2017

Evaluation of Diffusion Weighted Imaging in the Context of Multi-Parametric MRI of the Prostate in the assessment of suspected low volume prostatic carcinoma

Data from a multi-parametric MRI study of patients with possible early-stage prostate cancer was assessed with a view to creating an efficient clinical protocol. Based on a correlation analysis suggesting that diffusion-weighted imaging (DWI) scores are more strongly correlated with overall PIRADS scores than other modalities such as dynamic contrast enhanced imaging or spectroscopy, we investigate the combination of T2-weighted imaging (T2w) and DWI as a potential diagnostic tool for prostate cancer detection, staging and guided biopsies. Quantification of the noise floor in the DWI images and careful fitting of the data suggests that the mono-exponential model provides a very good fit to the data and there is no evidence of non-Gaussian diffusion for $b$-values up to 1000 s/mm$^2$. This precludes the use of kurtosis or other non-Gaussian measures as a biomarker for prostate cancer in our case. However, the ADC scores for healthy and probably malignant regions are significantly lower for the latter in all 20 but one patient. The results suggest that a simplified mp-MRI protocol combining T2w and DWI may be a good compromise for a cost and time efficient, early-stage prostate cancer diagnostic programme, combining robust MR biomarkers for prostate cancer that can be reliably quantified and appear well-suited for general clinical practice.

physics.med-ph↗
arXiv2017

Comparison of CPMG and Uhrig Dynamic Decoupling (UDD) for tissue refocusing in MRI

Two different dynamic decoupling strategies, the classic CPMG and the more recently proposed UDD protocol are compared in the context of magnetic resonance imaging (MRI). Both sequences were implemented on a 3T human MRI system and relaxometry was performed for a variety of tissue-mimicking agar and agarose gels. We find that CPMG provides moderately better decoupling than \UDD. The results are consistent with experimental noise spectra obtained from \textit{in vivo} spectroscopy results, which suggest that the type of noise spectra obtained would favor \CPMG. Theoretical coherence pathway analysis further suggests that \UDD\ is more susceptible to systematic errors due to static magnetic and radio-frequency field inhomogeneity or imperfect excitation and refocusing pulse profiles.

physics.med-ph↗
arXiv2016

Design and Characterisation of Tissue-Mimicking Gel Phantoms for Diffusion Kurtosis Imaging

Purpose: The aim of this work was to create tissue-mimicking gel phantoms appropriate for diffusion kurtosis imaging (DKI) for quality assurance, protocol optimization and sequence development. Methods: A range of agar, agarose and polyvinyl alcohol phantoms with concentrations ranging from 1.0% to 3.5%, 0.5% to 3.0% and 10% to 20%, respectively, and up to 3 g of glass microspheres per 100 ml were created. Diffusion coefficients, excess kurtosis values and relaxation rates were experimentally determined. Results: The kurtosis values for the plain gels ranged from 0.05 with 95% confidence interval (CI) of $(0.029, 0.071)$ to $0.216(0.185, 0.246)$, well below the kurtosis values reported in the literature for various tissues. The addition of glass microspheres increased the kurtosis of the gels with values up to $0.523(0.465, 0.581)$ observed for gels with the highest concentration of microspheres. Repeat scans of some of the gels after more than six months of storage at room temperature indicate changes in the diffusion parameters of less than 10%. The addition of the glass microspheres reduces the apparent diffusion coefficients (ADCs) and increases the longitudinal and transverse relaxation rates but the values remain comparable to those for plain gels and tissue, with ADCs observed ranging from $818(585, 1053) \times 10^{-6}$ mm$^2$/s to $2257(2118, 2296) \times 10^{-6}$ mm$^2$/s, and R1 values ranging from $0.34(0.32, 0.35)$ 1/s to $0.51(0.50, 0.52)$ 1/s, and R2 values ranging from $9.69(9.34, 10.04)$ 1/s to $33.07(27.10, 39.04)$ 1/s. Conclusions: Glass microspheres can be used to effectively modify diffusion properties of gel phantoms and achieve a range of kurtosis values comparable to those reported for a variety of tissues.

physics.med-ph↗
arXiv2014

Super Dielectric Materials

Evidence is provided that a class of materials with dielectric constants greater than 100,000, herein called super dielectric materials (SDM), can be generated readily from common, inexpensive materials.

cond-mat.mtrl-sci↗
arXiv2011

Phase behaviour of binary mixtures of diamagnetic colloidal platelets in an external magnetic field

Using fundamental measure density functional theory we investigate paranematic-nematic and nematic-nematic phase coexistence in binary mixtures of circular platelets with vanishing thicknesses. An external magnetic field induces uniaxial alignment and acts on the platelets with a strength that is taken to scale with the platelet area. At particle diameter ratio lambda=1.5 the system displays paranematic-nematic coexistence. For lambda=2, demixing into two nematic states with different compositions also occurs, between an upper critical point and a paranematic-nematic-nematic triple point. Increasing the field strength leads to shrinking of the coexistence regions. At high enough field strength a closed loop of immiscibility is induced and phase coexistence vanishes at a double critical point above which the system is homogeneously nematic. For lambda=2.5, besides paranematic-nematic coexistence, there is nematic-nematic coexistence which persists and hence does not end in a critical point. The partial orientational order parameters along the binodals vary strongly with composition and connect smoothly for each species when closed loops of immiscibility are present in the corresponding phase diagram.

cond-mat.soft↗
arXiv2010

Bulk phase behaviour of binary hard platelet mixtures from density functional theory

We investigate isotropic-isotropic, isotropic-nematic and nematic-nematic phase coexistence in binary mixtures of circular platelets with vanishing thickness, continuous rotational degrees of freedom and radial size ratios $\lambda$ up to 5. A fundamental measure density functional theory, previously used for the one-component model, is proposed and results are compared against those from Onsager theory as a benchmark. For $\lambda \leq 1.7$ the system displays isotropic-nematic phase coexistence with a widening of the biphasic region for increasing values of $\lambda$. For size ratios $\lambda \geq 2$, we find demixing into two nematic states becomes stable and an isotropic-nematic-nematic triple point can occur. Fundamental measure theory gives a smaller isotropic-nematic biphasic region than Onsager theory and locates the transition at lower densities. Furthermore, nematic-nematic demixing occurs over a larger range of compositions at a given value of $\lambda$ than found in Onsager theory. Both theories predict the same topologies of the phase diagrams. The partial nematic order parameters vary strongly with composition and indicate that the larger particles are more strongly ordered than the smaller particles.

cond-mat.soft↗
arXiv2008

Selective Atomic Heating in Plasmas: Implications for Quantum Theory

A new model of quantum mechanics, Classical Quantum Mechanics, is based on the (nearly heretical) postulate that electrons are physical objects that obey classical physical laws. Indeed, ionization energies, excitation energies etc. are computed based on picturing electrons as bubbles of charge that symmetrically surround a nucleus. Hence, for example, simple algebraic expressions based on Newtonian force balances are used to predict ionization energies and stable excitation states with remarkable precision. One of the most startling predictions of the model is that there are stable sizes of the hydrogen atom electron (bubble diameter) that are smaller (called hydrinos) than that calculated for the standard ground state. Experimental evidence in support of this novel physical/classical version of quantum is alleged to be found in the existence of super heated hydrogen atoms reported by many teams in a variety of plasmas. It is postulated that the energy required for creating super heated H aoms comes from the shrinkage of ground state H atoms to form hydrinos. This claim is discussed with reference to a brief review of the published studies of line broadening.

physics.plasm-ph↗
arXiv2006

Increasing Exclusion: The Pauli Exclusion Principle and Energy Conservation for Bound Fermions are Mutually Exclusive

A review of those forms of standard quantum mechanics that include the Pauli Exclusion Principle as it is applied to atomic species, (that is versions of quantum that are multi-electron and multi-orbital) shows they are not consistent with energy conservation. Particular focus is given to helium in which it is shown that energy conservation is not consistent with current models. If the two electrons in the ground state, per current theory, are at the same energy as the ionization energy, it is demonstrated that according to the standard theory approximately 30 eV are lost during ionization, or alternatively, about 30 eV of energy are created during ionization/electron attachment. The same issue of energy loss during relaxation of energy levels following ionization is shown to exist for all atomic species, thus demonstrating that the Pauli Exclusion Principle (PEP) and energy conservation are not consistent for any atomic species for current forms of distinguishable electron forms of quantum theory. Only that form of quantum that has a single orbital, and for which only one ionization energy can be computed (that is the original Schrodinger form), is consistent with an energy balance. However, this form is not consistent with common spectroscopy results, and it is argued PEP has no meaning in this form of quantum theory. In contrast a new model, Classical Quantum Mechanics (CQM), invented by R. Mills,, following modification, is consistent with all spectroscopy and energy conservation for bound electron systems. This new model is based on the validity of Maxwell s Equations and Newton s Laws at all scales. Detailed, and remarkably simple, computations for determining the ground state energy levels in one and two electron systems using CQM are presented. Agreements with data are excellent.

physics.gen-ph↗
arXiv2005

Evidence of Catalytic Production of Hot Atomic Hydrogen in RF Generated Hydrogen/Helium Plasmas

A study of the line shapes of hydrogen Balmer series lines in RF generated low pressure H2/He plasmas produced results suggesting a catalytic process between helium and hydrogen species results in the generation of 'hot' (ca. 28 eV) atomic hydrogen. Even far from the electrodes 'hot' atomic hydrogen was predominant in H2/He plasmas. Line shapes, relative line areas of cold and hot atomic hydrogen (hot/cold>2.5), were very similar for areas between the electrodes and far from the electrodes for these plasmas. In contrast, in H2/Xe only 'warm' (<5 eV) hydrogen (warm/cold<1.0) was found between the electrodes, and only cold hydrogen away from the electrodes. Earlier postulates that preferential hydrogen line broadening in plasmas results from the acceleration of ionic hydrogen in the vicinity of electrodes, and the special charge exchange characteristics of Ar/H2+ are clearly belied by the present results that show atomic hydrogen line shape are similar for H2/He plasmas throughout the relatively large cylindrical (14 cm ID x 36 cm length) cavity.

physics.plasm-ph↗
arXiv2005

Evidence of the production of hot hydrogen atoms in RF plasmas by catalytic reactions between hydrogen and oxygen species

Selective H-atom line broadening was found to be present throughout the volume (13.5 cm ID x 38 cm length) of RF generated H2O plasmas in a GEC cell. Notably, at low pressures (ca. <0.08 Torr), a significant fraction (ca. 20%) of the atomic hydrogen was 'hot' with energies greater than 40 eV with a pressure dependence, but only a weak power dependence. The degree of broadening was virtually independent of the position studied within the GEC cell, similar to the recent finding for He/H2 and Ar/H2 plasmas in the same GEC cell. In contrast to the atomic hydrogen lines, no broadening was observed in oxygen species lines at low pressures. Also, in control Xe/H2 plasmas run in the same cell at similar pressures and adsorbed power, no significant broadening of atomic hydrogen, Xe, or any other lines was observed. Stark broadening or acceleration of charged species due to high electric fields can not explain the results since (i) the electron density was insufficient by orders of magnitude, (ii) the RF field was essentially confined to the cathode fall region in contrast to the broadening that was independent of position, and (iii) only the atomic hydrogen lines were broadened. Rather, all of the data is consistent with a model that claims specific, predicted, species can act catalytically through a resonant energy transfer mechanism to create hot hydrogen atoms in plasmas.

physics.plasm-ph↗
arXiv2005

Evidence of catalytic production of hot hydrogen in rf generated hydrogen/argon plasmas

In this paper the selective broadening of the atomic hydrogen lines in pure H2 and Ar/H2 mixtures in a large 'GEC' cell (36 cm length_ 14 cm ID) was mapped as a function of position, H2/Ar ratio, time, power, and pressure. Several observations regarding the selective line broadening were particularly notable as they are unanticipated on the basis of earlier models. First, the anomalous broadening of the Balmer lines was found to exist throughout the plasma, and not just in the region between the electrodes. Second, the broadening was consistently a complex function of the operating parameters particularly gas composition (highest in pure H2), position, power, time and pressure. Clearly not anticipated by earlier models were the findings that under some conditions the highest concentration of 'hot' (>10 eV) hydrogen was found at the entry end, and not in the high field region between the electrodes and that in other conditions, the hottest H was at the (exit) pump (also grounded electrode) end. Third, excitation and electron temperatures were less than one eV in all regions of the plasma not directly adjacent (>1mm) to the electrodes, providing additional evidence that the energy for broadening, contrary to standard models, is not obtained from the field. Fourth, in contrast to our earlier studies of hydrogen/helium and water plasmas, we found that in some conditions 98% of the atomic hydrogen was in the 'hot' state throughout the GEC-type cell. Virtually every operating parameter studied impacted the character of the hot H atom population, and clearly second and third order effects exist, indicating a need for experimental design. Some non-field mechanisms for generating hot hydrogen atoms, specifically those suggested by Mills' CQM model, are outlined.

physics.plasm-ph↗
arXiv2004

Spectroscopic study of unique line broadening and inversion in low-pressure microwave generated water plasmas

It was demonstrated that low pressure (~0.2 Torr) water vapor plasmas generated in a 10 mm inner diameter quartz tube with an Evenson microwave cavity show at least two features which are not explained by conventional plasma models. First, significant (> 0.25 nm) hydrogen Balmer_ line broadening, of constant width, up to 5 cm from the microwave coupler was recorded. Only hydrogen, and not oxygen, showed significant line broadening. This feature, observed previously in hydrogen-containing mixed gas plasmas generated with high voltage dc and rf discharges was explained by some researchers to result from acceleration of hydrogen ions near the cathode. This explanation cannot apply to the line broadening observed in the (electrodeless) microwave plasmas generated in this work, particularly at distances as great as 5 cm from the microwave coupler. Second, inversion of the line intensities of both the Lyman and Balmer series, again, at distances up to 5 cm from the coupler, were observed. The line inversion suggests the existence of a hitherto unknown source of pumping of the optical power in plasmas. Finally, it is notable that other aspects of the plasma including the OH* rotational temperature and low electron concentrations are quite typical of plasmas of this type.

physics.plasm-ph↗