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Zhongguo Yi Liao Qi Xie Za Zhi =... Jul 2023The proton treatment control system is the supporting software of the proton therapy device, which specifically coordinates and controls the status and work of each...
The proton treatment control system is the supporting software of the proton therapy device, which specifically coordinates and controls the status and work of each subsystem. In this study, the software architecture and hardware implementation of the proton treatment control system was developed and built a foundation for the overall debugging. Using C# programming language and WPF programming techniques, TCP network communication protocol specified by the proton treatment technical document and MVVM pattern in Windows system, the logic design and implementation of each level were studied. Meanwhile, the communication interface between the subsystems under TCP communication protocol was agreed. The logic design and research of the setup field and treatment field were carried out. And the User Interface was designed and developed using the above technology. The program realizes the communication and interaction between the proton treatment control system and each subsystem, so as to control and monitor the whole treatment process. The proton treatment control system provides a software basis for the remote overall debugging and on-line monitor and control of proton treatment device.
Topics: Protons; User-Computer Interface; Software; Computers; Logic
PubMed: 37580285
DOI: 10.3969/j.issn.1671-7104.2023.04.004 -
Physics in Medicine and Biology Aug 2022Proton computed tomography (CT) is similar to x-ray CT but relies on protons rather than photons to form an image. In its most common operation mode, the measured...
Proton computed tomography (CT) is similar to x-ray CT but relies on protons rather than photons to form an image. In its most common operation mode, the measured quantity is the amount of energy that a proton has lost while traversing the imaged object from which a relative stopping power map can be obtained via tomographic reconstruction. To this end, a calorimeter which measures the energy deposited by protons downstream of the scanned object has been studied or implemented as energy detector in several proton CT prototypes. An alternative method is to measure the proton's residual velocity and thus its kinetic energy via the time of flight (TOF) between at least two sensor planes. In this work, we study the RSP resolution, seen as image noise, which can be expected from TOF proton CT systems.We rely on physics models on the one hand and statistical models of the relevant uncertainties on the other to derive closed form expressions for the noise in projection images. The TOF measurement error scales with the distance between the TOF sensor planes and is reported as velocity error in ps/m. We use variance reconstruction to obtain noise maps of a water cylinder phantom given the scanner characteristics and additionally reconstruct noise maps for a calorimeter-based proton CT system as reference. We use Monte Carlo simulations to verify our model and to estimate the noise due to multiple Coulomb scattering inside the object. We also provide a comparison of TOF helium and proton CT.We find that TOF proton CT with 30 ps mvelocity error reaches similar image noise as a calorimeter-based proton CT system with 1% energy error (1 sigma error). A TOF proton CT system with a 50 ps mvelocity error produces slightly less noise than a 2% calorimeter system. Noise in a reconstructed TOF proton CT image is spatially inhomogeneous with a marked increase towards the object periphery. Our modelled noise was consistent with Monte Carlo simulated images. TOF helium CT offers lower RSP noise at equal fluence, but is less advantageous at equal imaging dose.This systematic study of image noise in TOF proton CT can serve as a guide for future developments of this alternative solution for estimating the residual energy of protons and helium ions after the scanned object.
Topics: Helium; Image Processing, Computer-Assisted; Monte Carlo Method; Phantoms, Imaging; Protons; Tomography, X-Ray Computed
PubMed: 35603758
DOI: 10.1088/1361-6560/ac7191 -
Nature Communications Jul 2021The green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric...
The green-light absorbing proteorhodopsin (GPR) is the archetype of bacterial light-driven proton pumps. Here, we present the 2.9 Å cryo-EM structure of pentameric GPR, resolving important residues of the proton translocation pathway and the oligomerization interface. Superposition with the structure of a close GPR homolog and molecular dynamics simulations reveal conformational variations, which regulate the solvent access to the intra- and extracellular half channels harbouring the primary proton donor E109 and the proposed proton release group E143. We provide a mechanism for the structural rearrangements allowing hydration of the intracellular half channel, which are triggered by changing the protonation state of E109. Functional characterization of selected mutants demonstrates the importance of the molecular organization around E109 and E143 for GPR activity. Furthermore, we present evidence that helices involved in the stabilization of the protomer interfaces serve as scaffolds for facilitating the motion of the other helices. Combined with the more constrained dynamics of the pentamer compared to the monomer, these observations illustrate the previously demonstrated functional significance of GPR oligomerization. Overall, this work provides molecular insights into the structure, dynamics and function of the proteorhodopsin family that will benefit the large scientific community employing GPR as a model protein.
Topics: Cryoelectron Microscopy; Gene Expression; Light; Molecular Dynamics Simulation; Physical Phenomena; Protein Conformation; Protons; Rhodopsin; Rhodopsins, Microbial
PubMed: 34226545
DOI: 10.1038/s41467-021-24429-6 -
Chemical Communications (Cambridge,... Feb 2023Biomarkers are essential in biology, physiology, and pharmacology; thus, their detection is of extensive importance. Fluorescent probes provide effective tools for... (Review)
Review
Biomarkers are essential in biology, physiology, and pharmacology; thus, their detection is of extensive importance. Fluorescent probes provide effective tools for detecting biomarkers exactly. Excited state intramolecular proton transfer (ESIPT), one of the significant photophysical processes that possesses specific photoisomerization between Keto and Enol forms, can effectively avoid annoying interference from the background with a large Stokes shift. Hence, ESIPT is an excellent choice for biomarker monitoring. Based on the ESIPT process, abundant probes were designed and synthesized using three major design methods. In this review, we conclude probes for 14 kinds of biomarkers based on ESIPT explored in the past five years, summarize these general design methods, and highlight their application for biomarker detection or .
Topics: Fluorescent Dyes; Protons
PubMed: 36723346
DOI: 10.1039/d2cc06556h -
Journal of the American Chemical Society Mar 2022Metalloproteins with active sites containing di-Fe cores exhibit diverse chemical reactivity that is linked to the precise transfer of protons and electrons which...
Metalloproteins with active sites containing di-Fe cores exhibit diverse chemical reactivity that is linked to the precise transfer of protons and electrons which directly involve the di-Fe units. The redox conversions are commonly corroborated by spectroscopic methods, but the associated structural changes are often difficult to assess, particularly those related to proton movements. This report describes the development of di-Fe complexes in which the movements of protons and electrons are pinpointed during the stepwise oxidation of a di-Fe species to one with an FeFe core. Complex formation was promoted using the phosphinic amido tripodal ligand [poat] (,',″-[nitrilotris(ethane-2,1-diyl)]tris(,-diphenylphosphinic amido)) that provided dynamic coordination spheres that assisted in regulating both electron and proton transfer processes. Oxidation of an [Fe-(μ-OH)-Fe] complex led to the corresponding di-Fe species containing a hydroxido bridge that was not stable at room temperature and converted to a species containing an oxido bridging ligand and protonation of one phosphinic amido group to form [Hpoat]. Deprotonation led to a new species with an [Fe-(μ-O)-Fe] core that could be further oxidized to its FeFe analogue. Reactions with phenols suggest homolytic cleavage of the O-H bond to give products that are consistent with the initial formation of a phenoxyl radical─spectroscopic studies indicated that the electron is transferred to the Fe center, and the proton is initially transferred to the more sterically hindered oxido ligand but then relocates to [poat]. These findings offer new mechanistic insights related to the stability of and the reactions performed by di-Fe enzymes.
Topics: Ferric Compounds; Ferrous Compounds; Ligands; Oxidation-Reduction; Protons
PubMed: 35192354
DOI: 10.1021/jacs.1c12888 -
Biophysical Chemistry Sep 2023The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic... (Review)
Review
The transmembrane-electrostatically localized protons (TELP) theory can serve as a unified framework to explain experimental observations and elucidate bioenergetic systems including both delocalized and localized protonic coupling. With the TELP model as a unified framework, it is now better explained how the bacteriorhodopsin-purple membrane-ATPase system functions. The bacteriorhodopsin pumping of protons across the membrane results in the formation of TELP around the halobacterial extracellular membrane surface that is perfectly positioned to drive ATP synthase for the synthesis of ATP from ADP and Pi. The bacteriorhodopsin purple membrane sheet experiment of Heberle et al. 1994 is now better explained here as a transient "protonic capacitor". During the lifetime of a flashlight-induced protonic bacteriorhodopsin purple membrane capacitor activity, there is at least a transient non-zero membrane potential (Δψ ≠ 0). The experimental results demonstrated that "after proton release by an integral membrane protein, long-range proton transfer along the membrane surface is faster than proton exchange with the bulk water phase" exactly as predicted by the TELP theory, which is fundamentally important to the science of bioenergetics.
Topics: Protons; Bacteriorhodopsins; Membrane Potentials; Adenosine Triphosphate
PubMed: 37406610
DOI: 10.1016/j.bpc.2023.107072 -
Chemphyschem : a European Journal of... Feb 2022Anhydrous silicophosphoric acid glass with an approximate composition of H Si P O was synthesized and its thermal and proton-conducting properties were characterized....
Anhydrous silicophosphoric acid glass with an approximate composition of H Si P O was synthesized and its thermal and proton-conducting properties were characterized. Despite exhibiting a glass transition at 192 °C, the supercooled liquid could be handled as a solid up to 280 °C owing to its high viscosity. The glass and its melt exhibited proton conduction with a proton transport number of ∼1. Although covalent O-H bonds were weakened by relatively strong hydrogen bonding, the proton conductivity (4×10 S cm at 276 °C) was considerably lower than that of phosphoric acid. The high viscosity of the melt was due to the tight cross-linking of phosphate ion chains by six-fold-coordinated Si atoms. The low proton conductivity was attributed to the trapping of positively charged proton carriers around anionic SiO units (expressed as (SiO ) ) to compensate for the negative charges.
Topics: Electric Conductivity; Glass; Hydrogen Bonding; Protons
PubMed: 34862847
DOI: 10.1002/cphc.202100840 -
Inorganic Chemistry Dec 2023Nitrogenase is the only enzyme that can cleave the strong triple bond in N, making nitrogen available for biological life. There are three isozymes of nitrogenase,...
Nitrogenase is the only enzyme that can cleave the strong triple bond in N, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe-Fe pairs. For the E state, we find that protonation of the S2B μ belt sulfide ion is most favorable, 14-117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.
Topics: Nitrogenase; Tricarboxylic Acids; Protons; Catalytic Domain
PubMed: 37987624
DOI: 10.1021/acs.inorgchem.3c02329 -
Biochemistry May 2023In photosynthetic reaction centers from purple bacteria (PbRCs), light-induced charge separation leads to the reduction of the terminal electron acceptor quinone, Q. The...
In photosynthetic reaction centers from purple bacteria (PbRCs), light-induced charge separation leads to the reduction of the terminal electron acceptor quinone, Q. The reduction of Q to Q is followed by protonation via Asp-L213 and Ser-L223 in PbRC from . However, Asp-L213 is replaced with nontitratable Asn-L222 and Asn-L213 in PbRCs from and , respectively. Here, we investigated the energetics of proton transfer along the asparagine-involved H-bond network using a quantum mechanical/molecular mechanical approach. The potential energy profile for the H-bond between HO and the carbonyl O site of Asn-L222 shows that the proton is predominantly localized at the Asn-L222 moiety in the PbRC protein environment, easily forming the enol species. The release of the proton from the amide -NH site toward Ser-L232 via tautomerization suffers from the energy barrier. Upon reorientation of Asn-L222, the enol -OH site forms a short low-barrier H-bond with Ser-L232, facilitating protonation of Q in a Grotthuss-like mechanism. This is a basis of how asparagine or glutamine side chains function as acceptors/donors in proton transfer pathways.
Topics: Protons; Electron Transport; Oxidation-Reduction; Asparagine; Photosynthetic Reaction Center Complex Proteins; Mutagenesis, Site-Directed; Rhodobacter sphaeroides; Kinetics
PubMed: 37083399
DOI: 10.1021/acs.biochem.3c00013 -
Molecules (Basel, Switzerland) Oct 20195-Fluorouracil (5FU), a common anti-cancer drug, occurs in four tautomeric forms and possesses two potential sites of both protonation and deprotonation. Tautomeric and...
5-Fluorouracil (5FU), a common anti-cancer drug, occurs in four tautomeric forms and possesses two potential sites of both protonation and deprotonation. Tautomeric and resonance structures of the ionized forms of 5FU create the systems of connected equilibriums. Since there are contradictory reports on the ionized forms of 5FU in the literature, complex theoretical studies on neutral, protonated and deprotonated forms of 5FU, based on the broad spectrum of DFT methods, are presented. These indicate that the O4 oxygen is more willingly protonated than the O2 oxygen and the N1 nitrogen is more willingly deprotonated than the N3 nitrogen in a gas phase. Such preferences are due to advantageous charge delocalization of the respective ions, which is demonstrated by the NBO and ESP analyses. In an aqueous phase, stability differences between respective protonated and deprotonated forms of 5FU are significantly diminished due to the competition between the mesomeric effect and solvation. The calculated p values of the protonated, neutral and singly deprotonated 5FU indicate that 5FU does not exist in the protonated and double-deprotonated forms in the pH range of 0-14. The neutral form dominates below pH 8 and the N1 deprotonated form dominates above pH 8.
Topics: Fluorouracil; Hydrogen Bonding; Hydrogen-Ion Concentration; Molecular Structure; Nitrogen; Oxygen; Protons; Water
PubMed: 31614932
DOI: 10.3390/molecules24203683