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At least 1,495 records · Page 83

cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism

The cMonkey integrated biclustering algorithm identifies conditionally co-regulated modules of genes (biclusters). cMonkey integrates various orthogonal pieces of information which support evidence of gene co-regulation, and optimizes biclusters to be supported simultaneously by one or more of these prior constraints. The algorithm served as the cornerstone for constructing the first global, predictive Environmental Gene Regulatory Influence Network (EGRIN) model for a free-living cell, and has now been applied to many more organisms. However, due to its computational inefficiencies, long run-time and complexity of various input data types, cMonkey was not readily usable by the wider community. To address these primary concerns, we have significantly updated the cMonkey algorithm and refactored its implementation, improving its usability and extendibility. These improvements provide a fully functioning and user-friendly platform for building co-regulated gene modules and the tools necessary for their exploration and interpretation. We show, via three separate analyses of data for E. coli, M. tuberculosis and H. sapiens, that the updated algorithm and inclusion of novel scoring functions for new data types (e.g. ChIP-seq and transcription factor over-expression [TFOE]) improve discovery of biologically informative co-regulated modules. The complete cMonkey2 software package, including source code, is available at https://github.com/baliga-lab/cmonkey2.

59 BASIC BIOLOGICAL SCIENCES↗

Affinity maturation of a portable Fab–RNA module for chaperone-assisted RNA crystallography

Antibody fragments such as Fabs possess properties that can enhance protein and RNA crystallization and therefore can facilitate macromolecular structure determination. In particular, Fab BL3–6 binds to an AAACA RNA pentaloop closed by a GC pair with ~100 nM affinity. The Fab and hairpin have served as a portable module for RNA crystallization. The potential for general application make it desirable to adjust the properties of this crystallization module in a manner that facilitates its use for RNA structure determination, such as ease of purification, surface entropy or binding affinity. In this work, we used both in vitro RNA selection and phage display selection to alter the epitope and paratope sides of the binding interface, respectively, for improved binding affinity. We identified a 5'-GNGACCC-3' consensus motif in the RNA and S97N mutation in complimentarity determining region L3 of the Fab that independently impart about an order of magnitude improvement in affinity, resulting from new hydrogen bonding interactions. Using a model RNA, these modifications facilitated crystallization under a wider range of conditions and improved diffraction. The improved features of the Fab–RNA module may facilitate its use as an affinity tag for RNA purification and imaging and as a chaperone for RNA crystallography.

59 BASIC BIOLOGICAL SCIENCES↗

SENSEI: A Search for Diurnal Modulation in Sub-GeV Dark Matter Scattering

Dark matter particles with sufficiently large interactions with ordinary matter can scatter in the Earth’s atmosphere and crust before reaching an underground detector. This Earth-shielding effect can induce a directional dependence in the dark matter flux, leading to a sidereal daily modulation in the signal rate. We perform a search for such a modulation using data from the SENSEI experiment, targeting MeV-scale dark matter. We achieve nearly an order-of-magnitude improvement in sensitivity over previous direct-detection bounds for dark-matter masses below ∼ 1 MeV , assuming the standard halo model with a Maxwell-Boltzmann velocity distribution, and restrict the amplitude of a general daily modulation signal to be below 6.8 e / g / d .

Bloch, Itay M. [UC, Berkeley; LBL, Berkeley]↗

Three-dimensional lattice modulations in the charge density wave system Lu 2 Ir 3 Si 5

Using total and resonant x-ray scattering coupled to large-scale computer modeling, we study the lattice modulations in the complex charge density wave (CDW) material Lu 2 ⁢Ir 3 ⁢Si 5 . Here, we find that it is a unique quantum system where periodic lattice modulations related to emergent CDW order occur in three orthogonal atomic planes of the crystal lattice, leading to the emergence of an unusual three-dimensional (3D) pattern of short and long Ir-Ir and Lu-Lu bonds. The 3D character of observed lattice modulations explains the largely isotropic character of the changes in the electronic properties occurring when the CDW order sets in, demonstrating the strong electron-lattice coupling in Lu 2 ⁢Ir 3 ⁢Si 5 . The result is supported by DFT calculations based on the experimental structure data. Altogether, our work provides strong evidence for the presence of a relationship between the dimensionality of emergent lattice distortions and that of concurrent changes in the electronic properties of CDW materials. The relationship may need to be accounted for when these materials are explored for practical applications.

36 MATERIALS SCIENCE↗

Coherent control of molecular rotational state populations by periodic phase-step modulation

We theoretically demonstrate that the molecular rotational state populations through an impulsive nonresonant Raman process can be manipulated by shaping the femtosecond laser pulse with a periodic phase-step modulation. We show that, by precisely controlling these parameters characterizing the periodic phase-step modulation, both the odd and even rotational state populations can be completely suppressed or reconstructed as that induced by the transform-limited laser pulse, and the relative excitation between the odd and even rotational state populations can also be obtained. Furthermore, we show that the field-free molecular alignment can be manipulated due to the modulation of the odd and even rotational state populations.

74 ATOMIC AND MOLECULAR PHYSICS↗

Photoassociation dynamics driven by a modulated two-color laser field

Photoassociation (PA) dynamics of ultracold cesium atoms steered by a modulated two-color laser field E(t)=E{sub 0}f(t)cos((2{pi}/T{sub p})-{phi})cos({omega}{sub L}t) is investigated theoretically by numerically solving the time-dependent Schroedinger equation. The PA dynamics is sensitive to the phase of envelope (POE) {phi} and the period of the envelope T{sub p}, which indicates that it can be controlled by varying POE {phi} and period T{sub p}. Moreover, we introduce the time- and frequency-resolved spectrum to illustrate how the POE {phi} and the period T{sub p} influence the intensity distribution of the modulated laser pulse and hence change the time-dependent population distribution of photoassociated molecules. When the Gaussian envelope contains a few oscillations, the PA efficiency is also dependent on POE {phi}. The modulated two-color laser field is available in the current experiment based on laser mode-lock technology.

74 ATOMIC AND MOLECULAR PHYSICS↗

Quantized vortices in a rotating Bose-Einstein condensate with spatiotemporally modulated interaction

We present theoretical analysis and numerical studies of the quantized vortices in a rotating Bose-Einstein condensate with spatiotemporally modulated interaction in harmonic and anharmonic potentials, respectively. The exact quantized vortex and giant vortex solutions are constructed explicitly by similarity transformation. Their stability behavior has been examined by numerical simulation, which shows that a new series of stable vortex states (defined by radial and angular quantum numbers) can be supported by the spatiotemporally modulated interaction in this system. We find that there exist stable quantized vortices with large topological charges in repulsive condensates with spatiotemporally modulated interaction. We also give an experimental protocol to observe these vortex states in future experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Passive state preparation in the Gaussian-modulated coherent-states quantum key distribution

In the Gaussian-modulated coherent-states (GMCS) quantum key distribution (QKD) protocol, Alice prepares quantum states actively: For each transmission, Alice generates a pair of Gaussian-distributed random numbers, encodes them on a weak coherent pulse using optical amplitude and phase modulators, and then transmits the Gaussian-modulated weak coherent pulse to Bob. Here we propose a passive state preparation scheme using a thermal source. In our scheme, Alice splits the output of a thermal source into two spatial modes using a beam splitter. She measures one mode locally using conjugate optical homodyne detectors, and transmits the other mode to Bob after applying appropriate optical attenuation. Under normal conditions, Alice's measurement results are correlated to Bob's, and they can work out a secure key, as in the active state preparation scheme. Given the initial thermal state generated by the source is strong enough, this scheme can tolerate high detector noise at Alice's side. Furthermore, the output of the source does not need to be single mode, since an optical homodyne detector can selectively measure a single mode determined by the local oscillator. Preliminary experimental results suggest that the proposed scheme could be implemented using an off-the-shelf amplified spontaneous emission source.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Charge density modulation and defect ordering in the $Na_xMnBi_y$ magnetic semimetal

The I-Mn-V antiferromagnet, NaMnBi, develops a very large positive magnetoresistance (MR) up to 10 000% at 2 K and 9 T in crystals showing a semiconductor-to-metal transition (SMT). In the absence of an SMT, a modest (20%) MR is achieved. Here, we show that upon cooling below the magnetic transition, a spatial modulation appears giving rise to new Bragg peaks due to charge and defect ordering in a checkerboard pattern, with two kinds of modulation vectors, $q_1 = \left( \frac{2}{3}, 0, 1 \right)$ and $q_2 = \left( \frac{2}{3}, \frac{1}{3}, \frac {1}{2} \right)$. This constitutes a superlattice transition ($T_s$) that lowers the symmetry from the high-temperature centrosymmetric $P4/nmm$ to the noncentrosymmetric $P\overline{4}m2$. In crystals with a large MR, a close to room temperature $T_s$ is observed with $q_1$ appearing first, followed by $q_2$. In crystals with low MR, however, $T_s$ is much lower and only $q_1$ is observed. Finally, the charge modulation and spin fluctuations may both contribute to the enhancement of MR.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Raman scattering of intense, short laser pulses in modulated plasmas

We examine the exponentiation of the Raman forward scattering instability in modulated plasma channels computationally and analytically. An evolution equation for the complex phases of the Raman scattered waves treating the spatial localization and discrete nature of the channel modes is derived. Simulations with WAKE [P. Mora and T. M. Antonsen Jr., Phys. Plasmas 4, 217 (1997)] verify the theory in the linear growth regime and provide insight into the nonlinear stage of the instability when cascading and pump depletion play a role. We find that the exponentiation in modulated channels depends on two factors: the increase in coupling due to the increased plasma wavenumber in the high-density regions of the channel and a decreased coupling due to the reduced longitudinal spatial coherence. For the parameters considered, simulations show that the finite extent of the pump pulse is more significant in determining the exponentiation than phase mixing due to the transverse variation of the channel. Both the theory and simulations confirm that modulated channels allow for the stable guiding of longer pulses than nonmodulated channels.

43 PARTICLE ACCELERATORS↗

Low-frequency wave modulations in an electronegative dusty plasma in the presence of charge variations

The effects of dust charge variations on low-frequency wave modulations in an electronegative dusty plasma are investigated. The dynamics of the modulated wave is governed by a nonlinear Schroedinger equation with a dissipative term. The dissipation arises due to the nonsteady (nonadiabatic) dust charge variations. Theoretical and numerical investigations predict the formation of dissipative bright (envelope) and dark solitons. The nonsteady charge-variation-induced dissipation reduces the modulational instability growth rate and introduces a characteristic time scale to observe bright solitons. Results are discussed in the context of electronegative dusty plasma experiments.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Hosing Instability Suppression in Self-Modulated Plasma Wakefields

We show that the hosing instability can be suppressed after the saturation of the self-modulation instability of a long particle bunch if the plasma density perturbation is linear. We derive scalings for maximum bunch tilts and seeds for the self-modulation instability to ensure stable propagation beyond saturation of self-modulation instability. Numerical solutions of the reduced hosing equations and three-dimensional particle-in-cell simulations confirm our analytical findings. Our results may also apply when a train of particle bunches or laser pulses excites a linear wake.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Photonic Refrigeration from Time-Modulated Thermal Emission

We develop theoretical and computational formalisms to describe thermal radiation from temporally modulated systems. We demonstrate that such a modulation results in a photon-based active cooling mechanism. This mechanism has a high thermodynamic performance that can approach the Carnot limit. Our work points to exciting new avenues in active, time-modulated control of thermal emission for cooling and energy harvesting applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Magnetic Damping Modulation in IrMn 3 / Ni 80 Fe 20 via the Magnetic Spin Hall Effect

Noncollinear antiferromagnets can have additional spin Hall effects due to the net chirality of their magnetic spin structure, which provides for more complex spin-transport phenomena compared to ordinary nonmagnetic materials. Here we investigated how ferromagnetic resonance of permalloy (Ni 80 Fe 20 ) is modulated by spin Hall effects in adjacent epitaxial IrMn 3 films. We observe a large dc modulation of the ferromagnetic resonance linewidth for currents applied along the [001] IrMn 3 direction. Furthermore, this very strong angular dependence of spin-orbit torques from dc currents through the bilayers can be explained by the magnetic spin Hall effect where IrMn 3 provides novel pathways for modulating magnetization dynamics electrically.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Search for Daily Modulation of MeV Dark Matter Signals with DAMIC-M

Dark matter (DM) particles with sufficiently large cross sections may scatter as they travel through Earth’s bulk. The corresponding changes in the DM flux give rise to a characteristic daily modulation signal in detectors sensitive to DM-electron interactions. Here, we report results obtained from the first underground operation of the DAMIC-M prototype detector searching for such a signal from DM with MeV-scale mass. A model-independent analysis finds no modulation in the rate of 1 e − events with sidereal period, where a DM signal would appear. We then use these data to place exclusion limits on DM in the mass range [ 0.53 , 2.7 ] MeV / c 2 interacting with electrons via a dark photon mediator. Taking advantage of the time-dependent signal we improve by ∼ 2 orders of magnitude on our previous limit obtained from the total rate of 1 e − events, using the same dataset. This daily modulation search represents the current strongest limit on DM-electron scattering via ultralight mediators for DM masses around 1 MeV / c 2 . Published by the American Physical Society 2024

Arnquist, I. (ORCID:0000000256438330)↗

Design of a low parasitic inductance SiC power module with double-sided cooling

In this paper, a low-parasitic inductance SiC power module with double-sided cooling is designed and compared with a baseline double-sided cooled module. With the unique 3D layout utilizing vertical interconnection, the power loop inductance is effectively reduced without sacrificing the thermal performance. Both simulations and experiments are carried out to validate the design. Q3D simulation results show a power loop inductance of 1.63 nH, verified by the experiment, indicating more than 60% reduction of power loop inductance compared with the baseline module. With 0Ω external gate resistance turn-off at 600V, the voltage overshoot is less than 9% of the bus voltage at a load of 44.6A.

Yang, Fei↗

Bond Wire Damage Detection and State of Health Estimation of a 1200V, 900A Dual Pack IGBT Power Module using the RL-Equivalent Circuit

Electrical and environmental stresses are the two dominant contributors in aging and failure of power semiconductor devices. Insulated gate bipolar junction transistors (IGBTs) and metal-oxide semiconductor field effect transistors (MOSFETs) are two most commonly used switching devices in power converter circuits. A significant portion of research effort is given in inventing innovative methods to estimate the degradation and fatigue in these devices. Until today, no other existing techniques can determine the number of lifted bond wires and their locations in a live IGBT module, although this information is extremely helpful to understand the overall state of health of an IGBT power module. In this paper, we have proposed a reflectometry-based technique to overcome this hurdle. The RL-equivalent circuit to represent a bond wire has been developed for the device under test and simulated in CST Studio Suite to measure the reflection amplitudes. Experimental results were obtained using a prototype reflectometry hardware, and both the simulation and experimental results have been compared. These results prove that with these two sets of measurements, it is possible to locate the aged device inside a module and detect the number of bond wire lift-offs associated to that device.

30 DIRECT ENERGY CONVERSION↗

Analysis and Evaluation of Thermally Annealed Pyrolytic Graphite Heat Spreader for Power Modules

Next generation power modules demand increased heat extraction capability along with reduced weight and volume. In this paper, thermally annealed pyrolytic graphite (TPG) is analyzed and compared with conventional materials used in power modules for thermal management. Fundamental properties of TPG are explained and compared with commonly used materials in power module heat spreaders and substrates. The encapsulated TPG based heat spreader is manufactured and compared with bulk copper in simulation and experimental based analysis. The results show that encapsulated TPG based heat spreader achieves more than 50% reduction in thermal resistance along with 48% reduction in weight in the heat spreader layer.

Gurpinar, Emre↗