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We have developed a deep learning based method to decode the protein-ligand interactions and predict their probability of binding. We use 3-Dimensional structure of proteins and ligand molecules with the ligand docked to the receptor and use the information at the interaction region to assess the binding of the protein-ligand complex.
Background: Recent data from genome-wide chromosome conformation capture analysis indicate that the human genome is divided into conserved megabase-sized self-interacting regions called topological domains. These topological domains form the regulatory backbone of the genome and are separated by regulatory boundary elements or barriers. Copy-number variations can potentially alter the topological domain architecture by deleting or duplicating the barriers and thereby allowing enhancers from neighboring domains to ectopically activate genes causing misexpression and disease, a mutational mechanism that has recently been termed enhancer adoption. Results: We use the Human Phenotype Ontology database to relate the phenotypes of 922 deletion cases recorded in the DECIPHER database to monogenic diseases associated with genes in or adjacent to the deletions. We identify combinations of tissue-specific enhancers and genes adjacent to the deletion and associated with phenotypes in the corresponding tissue, whereby the phenotype matched that observed in the deletion. We compare this computationally with a gene-dosage pathomechanism that attempts to explain the deletion phenotype based on haploinsufficiency of genes located within the deletions. Up to 11.8% of the deletions could be best explained by enhancer adoption or a combination of enhancer adoption and gene-dosage effects. Conclusions: Our results suggest that enhancer adoption caused by deletions of regulatory boundaries may contribute to a substantial minority of copy-number variation phenotypes and should thus be taken into account in their medical interpretation.
Most mitochondrial mRNAs are transcribed as polycistronic precursors that are cleaved by endonucleases to produce mature mRNA transcripts. However, recent studies have shown that mitochondrial transcripts in the kinetoplastid protozoan, Trypanosoma brucei, are transcribed individually. Also unlike most mitochondrial mRNAs, the 5' end of these transcripts harbor a triphosphate that is hydrolyzed. This modification is carried out by a putative Nudix hydrolase called MERS1. The Nudix motif in MERS1 is degenerate, lacking a conserved glutamic acid, thus it is unclear how it may bind its substrates and whether it contains a Nudix fold. To obtain insight into this unusual hydrolase, we determined structures of apo, GTP-bound and RNA-bound T. brucei MERS1 to 2.30 Å, 2.45 Å, and 2.60 Å, respectively. The MERS1 structure has a unique fold that indeed contains a Nudix motif. The nucleotide bound structures combined with binding studies reveal that MERS1 shows preference for RNA sequences with a central guanine repeat which it binds in a single-stranded conformation. The apo MERS1 structure indicates that a significant portion of its nucleotide binding site folds upon substrate binding. Finally, a potential interaction region for a binding partner, MERS2, that activates MERS1 was identified. The MERS2-like peptide inserts a glutamate near the missing Nudix acidic residue in the RNA binding pocket, suggesting how the enzyme may be activated. Thus, the combined studies reveal insight into the structure and enzyme properties of MERS1 and its substrate-binding activities.
A promising alternative to Gaussian beams for use in strong field science is Bessel–Gauss (BG or Bessel-like) laser beams, as they are easily produced with readily available optics and provide more flexibility of the spot size and working distances. Here we use BG beams produced with a lens-axicon optical system for higher-order harmonic generation (HHG) in a thin gas jet. The finite size of the interaction region allows for scans of the HHG yield along the propagation axis. Further, by measuring the ionization yield in unison with the extreme ultraviolet (XUV), we are able to distinguish regions of maximum ionization from regions of optimum XUV generation. This distinction is of great importance for BG fields, as the generation of BG beams with axicons often leads to oscillations of the on-axis intensity, which can be exploited for extended phase-matching conditions. We observed such oscillations in the ionization and XUV flux along the propagation axis for the first time. As is the case for Gaussian modes, the harmonic yield is not maximum at the point of highest ionization. Finally, despite Bessel beams having a hole in the center in the far field, the XUV beam is well collimated, making BG modes a great alternative when spatial filtering of the fundamental is desired.
We investigate the macroscopic physics of noncollinear high harmonic generation (HHG) at high pressures. Here, we make the first experimental demonstration of phase matching of noncollinear high-order-difference-frequency generation at ionization fractions above the critical ionization level, which normally sets an upper limit on the achievable cutoff photon energies. Additionally, we show that noncollinear high-order-sum-frequency generation requires much higher pressures for phase matching than single-beam HHG does, which mitigates the short interaction region in this geometry. We also dramatically increase the experimentally realized cutoff energy of noncollinear circularly polarized HHG, reaching photon energies of 90 eV. Finally, we achieve complete angular separation of high harmonic orders without the use of a spectrometer.
The Medium-energy Electron Ion Collider (MEIC) at JLab is designed to provide high luminosity and high polarization needed to reach new frontiers in the exploration of nuclear structure. The luminosity, exceeding 1033 cm-2s-1 in a broad range of the center-of-mass (CM) energy and maximum luminosity above 1034 cm-2s-1, is achieved by high-rate collisions of short small-emittance low-charge bunches made possible by high-energy electron cooling of the ion beam and synchrotron radiation damping of the electron beam. The polarization of light ion species (p, d, 3He) can be easily preserved and manipulated due to the unique figure-8 shape of the collider rings. A fully consistent set of parameters have been developed considering the balance of machine performance, required technical development and cost. This paper reports recent progress on the MEIC accelerator design including electron and ion complexes, integrated interaction region design, figure-8-ring-based electron and ion polarization schemes, RF/SRF systems and ERL-based high-energy electron cooling. Luminosity performance is also presented for the MEIC baseline design.
Long-range beam-beam (LRBB) interactions can be a source of emittance growth and beam losses in the LHC during physics and will become even more relevant with the smaller '* and higher bunch intensities foreseen for the High Luminosity LHC upgrade (HL-LHC), in particular if operated without crab cavities. Both beam losses and emittance growth could be mitigated by compensat-ing the non-linear LRBB kick with a correctly placed current carrying wire. Such a compensation scheme is currently being studied in the LHC through a demonstration test using current-bearing wires embedded into col-limator jaws, installed either side of the high luminosity interaction regions. For HL-LHC two options are considered, a current-bearing wire as for the demonstrator, or electron lenses, as the ideal distance between the particle beam and compensating current may be too small to allow the use of solid materials. This paper reports on the ongoing activities for both options, covering the progress of the wire-in-jaw collimators, the foreseen LRBB experiments at the LHC, and first considerations for the design of the electron lenses to ultimately replace material wires for HL-LHC.
We present an update on the lattice design of the electron ring of the Jefferson Lab Electron-Ion Collider (JLEIC). The electron and ion collider rings feature a unique figure-8 layout providing optimal conditions for preservation of beam polarization. The rings include two arcs and two intersecting long straight sections containing a low-beta interaction region (IR) with special optics for detector polarimetry, electron beam spin rotator sections, ion beam cooling sections, and RF-cavity sections. Recent development of the electron ring lattice has been focused on minimizing the beam emittance while providing an efficient non-linear chromaticity correction and large dynamic aperture. We describe and compare three lattice designs, from which we determine the best option.
Crabbing cavities are one of the technological landmark that will allow the LHC to optimize its per-formance and maximize its integrated luminosity by allowing a head-on collision between the bunches despite the non-zero crossing angle. A total of 8 crab cavities will be installed in the interaction region of each of the two experiments, ATLAS and CMS. In the last years, the two types of crab cavities were de-signed, built and tested under the US-LARP R&D pro-gram. Horizontal crabbing is obtained with a radio-frequency dipole cavity (RFD) designed by Old Do-minion University (ODU), SLAC and Fermilab (FNAL). In this paper a new mechanical design, that uses passive stiffeners, is presented. This design leads to a decrease of the Lorentz Force Detuning frequency shift, satisfy the requirements on pressure sensitivity, validate the structural integrity and increase the tuner sensitivity and the maximum elastic tuning range. Furthermore, it will be possible to greatly simplify the shape of the magnetic shield and Helium vessel with respect to the current design.
Superconducting-final-focus-quadrupole magnet system (QCS) were installed on an interaction region (IR) of SuperKEKB on Feb. 2017. The QCS consists of eight quadrupole magnets and four compensation solenoids; these magnets are contained in the two cryostats and are installed into Belle II detector which generates a solenoid field of 1.5 T. We determined the quadrupole centers with respect to accelerator beam lines with a single stretched wire (SSW) method. Here the results of the magnetic measurement with SSW are presented.
Design of the electron and ion rings of the Jefferson Lab Electron-Ion Collider (JLEIC) features the low-beta Interaction Regions (IR) with detector solenoid, non-linear chromaticity compensation blocks (CCB), and spin rotator optics with solenoids. The high beta functions in the IR final focus quadrupoles (FFQ) and in the CCB magnets result in strong effects of errors in these magnets. Performance of the spin rotators may also be sensitive to the errors. The first part of this study includes the design of orbit correction system for both rings and evaluation of dynamic aperture (DA) with misalignment and the correction. The second part is devoted to the DA study with the FFQ non-linear field errors. The orbit correction design, the dynamic aperture, and the impact on error specifications are presented.
Crab crossing scheme is the essential scheme that accommodates large crossing angle without loss of luminosity in the design of Electron-Ion collider (EIC). The ideal optics and phase advances of the crab cavity pair are set to create a local crabbing bump in the interaction region (IR). However, there are always small errors in the actual lattice of IR. In this article, we will present the simulation and analytical studies on the imperfections in the crab crossing scheme in the EIC design. The tolerance of the imperfection and the possible remedies can be concluded from these studies.
In this work we show the final iteration of the design for the booster complex of the Jefferson Lab EIC, which would have brought the ions from an energy (proton) of 150 MeV up to 12.1 GeV. This complex would have consisted of two figure-8 rings. The Low Energy Booster (LEB) which would have accelerated its protons from 150 MeV to 8 GeV, and has had its lattice tweaked to increase the effectiveness of chromaticity cancellations. The High Energy Booster (HEB) would have brought the 8 GeV protons up to 12.1 GeV. The HEB would in the tunnel that was designed for the collider rings, sitting on top of them. It has had a bypass around the interaction region added, as well as a cooling solenoid installed.
The Electron-Ion Collider (EIC) is aiming at a design luminosity of 1e34 cm⁻²s⁻¹. To maintain such a high luminosity, both beams in the EIC need an acceptable beam lifetime in the presence of the beam-beam interaction. For this purpose, we carried out weak-strong element-by-element particle tracking to evaluate the long-term dynamic aperture for the hadron ring lattice design. We improved our simulation code SimTrack to treat some new lattice design features, such as radially offset on-momentum orbits, coordinate transformations in the interaction region, etc. In this article, we will present the preliminary dynamic aperture calculation results with β^{*}- function scan, radial orbit shift, crossing angle collision, and magnetic field errors.
The Electron-Ion Collider (EIC) is being designed for construction at Brookhaven National Laboratory. Activities have been focused on beam-beam simulations, polarization studies, and beam dynamics, as well as on maturing the layout and lattice design of the constituent accelerators and the interaction region. The latest design advances will be presented.
The Interaction Regions (IR) of many colliders benefit from the application of leading-edge technologies to ensure the highest possible luminosity delivered to the experiments. Leading-edge low-beta focusing magnets and crab cavities to handle individual bunches are critically important to increase the instantaneous and integrated luminosity in future Colliders.The High-Luminosity LHC Upgrade, HL-LHC, with Nb3Sn Magnets (called MQXF) and Superconducting Radio Frequency (SRF) crab cavities (of two types, called DQW and RFD) is a world-wide collaborative project under construction in this decade to utilize the solutions mentioned above as key ingredients to increase tenfold the integrated luminosity delivered to the CMS and ATLAS experiments in the next decade. The HL-LHC AUP is the US effort to contribute approximately 50% of the low-beta focusing magnets and crab cavities for the HL-LHC.In this contribution we present the valuable lessons learned by the US efforts in the procurement, construction, and testing phases of the Nb3Sn focusing magnets and SRF crab cavities. We will report on the experience gathered by HL-LHC AUP in the production of the first half of deliverables (magnets MQXFA03 to MQXFA13). We will also report on the test of the first cryoassemblies and the status of the cavities’ development, production and testing.Both the technical and project management lessons-learned will inform applications of these technologies to future colliders and projects.
The MQXFB magnets are superconducting quadrupoles with nominal peak field on the conductor of 11.3 T. With their magnetic length of 7.2 m, they stand as the longest Nb3Sn accelerator magnets designed and manufactured up to now. Together with the companion MQXFA 4.2 m long units, built by the US Accelerator Research Program, they are at the heart of HL-LHC, as they shall replace the inner triplet quadrupoles at either side of the ATLAS and CMS interaction regions of the LHC. This technology has benefited from many years of development, and this specific design was validated with successful short models (MQXFS, 1.2 m long). More recently, several MQXFA magnets were shown to satisfy HL-LHC requirements. In this paper, we report on the cold test results of four MQXFB magnets, focusing on performance, training, behavior after thermal and powering cycles, and field quality. We then provide an update of the overall status, including ongoing verifications of design changes at the level of the coil fabrication.
We present a Fixed-Field-Alternating (FFA) permanent magnet racetrack electron accelerator with energy range between 10-60 GeV for the future LHeC. Electron beam is brought back to the linac by the single beam line without requiring electric power REDUCING estimated wall power of 100 MW in the present LHeC design to a negligible power for arcs as the permanent magnets are used. The design is based on experience from the very successful commissioning of the Cornell University and Brookhaven National Laboratory Energy Recovery Test Accelerator ? ?CBETA?. The proposal supports sustainability efforts for LHeC by making a 'green' accelerator. It is an energy recovery linac with 99.9% energy efficiency and reduces the power consumption by using small permanent magnets. The FFA non-linear gradient design is a racetrack shape, where, as in the CBETA, the arcs are matched by adiabatic transition to the two (LHeC) or multiple straight sections. Two 10 GeV superconducting linacs are placed on both sides of the Interaction Region (IR) significantly reducing the power of synchrotron radiation loss.