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Single Flux Quantum Circuit Operation at Millikelvin Temperatures
Authors:
Jason Walter,
Adam C. Weis,
Kan-Ting Tsai,
Meng-Ju Yu,
Naveen Katam,
Alex F. Kirichenko,
Oleg A. Mukhanov,
Shu-Jen Han,
Igor V. Vernik
Abstract:
As quantum computing processors increase in size, there is growing interest in developing cryogenic electronics to overcome significant challenges to system scaling. Single flux-quantum (SFQ) circuits offer a promising alternative to remote, bulky, and power-hungry room temperature electronics. To meet the need for digital qubit control, readout, and co-processing, SFQ circuits must be adapted to…
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As quantum computing processors increase in size, there is growing interest in developing cryogenic electronics to overcome significant challenges to system scaling. Single flux-quantum (SFQ) circuits offer a promising alternative to remote, bulky, and power-hungry room temperature electronics. To meet the need for digital qubit control, readout, and co-processing, SFQ circuits must be adapted to operate at millikelvin temperatures near quantum processors. SEEQC's SFQuClass digital quantum management approach proximally places energy-efficient SFQ (ERSFQ) circuits and qubits in a multi-chip module. This enables extremely low power dissipation, compatible with a typical dilution cryostat's limited cooling power, while maintaining high processing speed and low error rates. We report on systematic testing from 4 K to 10 mK of a comprehensive set of ERSFQ cells, as well as more complex circuits such as programmable counters and demultiplexers used in digital qubit control. We compare the operating margins and error rates of these circuits and find that, at millikelvin, bias margins decrease and the center of the margins (i.e., the optimal bias current value) increases by ~15%, compared to 4.2 K. The margins can be restored by thermal annealing by reducing Josephson junction (JJ) critical current Ic. To provide guidance for how circuit parameters vary from 4.2 K to millikelvin, relevant analog process control monitors (PCMs) were tested in the temperature range of interest. The measured JJ critical current (of the PCM JJ arrays) increases by ~15% when decreasing temperature from 4.2 K to millikelvin, in good agreement with both theory and the empirically measured change in the center of bias margins for the tested digital circuits.
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Submitted 7 December, 2025;
originally announced December 2025.
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Navigating Chemical Space: Multi-Level Bayesian Optimization with Hierarchical Coarse-Graining
Authors:
Luis J. Walter,
Tristan Bereau
Abstract:
Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening methods. To approach chemical space exploration more effectively, we have developed an active learning-based method that uses transferable coarse-grained models to compress chemical space into varying levels of resoluti…
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Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening methods. To approach chemical space exploration more effectively, we have developed an active learning-based method that uses transferable coarse-grained models to compress chemical space into varying levels of resolution. By using multiple representations of chemical space with different coarse-graining resolutions, we balance combinatorial complexity and chemical detail. To identify target compounds, we first transform the discrete molecular spaces into smooth latent representations. We then perform Bayesian optimization within these latent spaces, using molecular dynamics simulations to calculate target free energies of the coarse-grained compounds. This multi-level approach effectively balances exploration and exploitation at lower and higher resolutions, respectively. We demonstrate the effectiveness of our method by optimizing molecules to enhance phase separation in phospholipid bilayers. Our funnel-like strategy not only suggests optimal compounds but also provides insight into relevant neighborhoods in chemical space. We show how this neighborhood information from lower resolutions can guide the optimization at higher resolutions, thereby providing an efficient way to navigate large chemical spaces for free energy-based molecular optimization.
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Submitted 15 July, 2025; v1 submitted 7 May, 2025;
originally announced May 2025.
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Search for Axionlike Dark Matter Using Liquid-State Nuclear Magnetic Resonance
Authors:
Julian Walter,
Olympia Maliaka,
Yuzhe Zhang,
John Blanchard,
Gary Centers,
Arian Dogan,
Martin Engler,
Nataniel L. Figueroa,
Younggeun Kim,
Derek F. Jackson Kimball,
Matthew Lawson,
Declan W. Smith,
Alexander O. Sushkov,
Dmitry Budker,
Hendrik Bekker,
Arne Wickenbrock
Abstract:
We search for dark matter in the form of axionlike particles (ALPs) in the mass range $5.576741 \,\mathrm{neV/c^2}$ - $5.577733\,\mathrm{neV/c^2}$ by probing their possible coupling to fermion spins through the ALP field gradient. This is achieved by performing proton nuclear magnetic resonance spectroscopy on a sample of methanol as a technical demonstration of the Cosmic Axion Spin Precession Ex…
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We search for dark matter in the form of axionlike particles (ALPs) in the mass range $5.576741 \,\mathrm{neV/c^2}$ - $5.577733\,\mathrm{neV/c^2}$ by probing their possible coupling to fermion spins through the ALP field gradient. This is achieved by performing proton nuclear magnetic resonance spectroscopy on a sample of methanol as a technical demonstration of the Cosmic Axion Spin Precession Experiment Gradient (CASPEr-Gradient) Low-Field apparatus. Searching for spin-coupled ALP dark matter in this mass range with associated Compton frequencies in a 240 Hz window centered at 1.348570 MHz resulted in a sensitivity to the ALP-proton coupling constant of $g_{\mathrm{ap}} \approx 3 \times 10^{-2}\,\mathrm{GeV}^{-1}$. This narrow-bandwidth search serves as a proof-of-principle and a commissioning measurement, validating our methodology and demonstrating the experiment's capabilities. CASPEr-Gradient Low-Field will probe the mass range from $4.1\,\mathrm{\peV/c^2}$ to $17\,\mathrm{\neV/c^2}$ with hyperpolarized samples to boost the sensitivity beyond the astronomical limits.
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Submitted 30 August, 2025; v1 submitted 22 April, 2025;
originally announced April 2025.
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Martignac: Computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations
Authors:
Tristan Bereau,
Luis J. Walter,
Joseph F. Rudzinski
Abstract:
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an acyclic directed graph, providing the entire history of a simulation -- from system preparation to p…
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Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: computational workflows for the coarse-grained (CG) Martini force field. Martignac describes Martini CG MD simulations as an acyclic directed graph, providing the entire history of a simulation -- from system preparation to property calculations. Martignac connects to NOMAD, such that all simulation data generated are automatically normalized and stored according to the FAIR principles. We present several prototypical Martini workflows, including system generation of simple liquids and bilayers, as well as free-energy calculations for solute solvation in homogeneous liquids and drug permeation in lipid bilayers. By connecting to the NOMAD database to automatically pull existing simulations and push any new simulation generated, Martignac contributes to improving the sustainability and reproducibility of molecular simulations.
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Submitted 23 September, 2024;
originally announced September 2024.
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A diamond anvil microassembly for Joule heating and electrical measurements up to 150 GPa and 4000 K
Authors:
Zachary M. Geballe,
Suzy M. Vitale,
Jing Yang,
Francesca Miozzi,
Vasilije V. Dobrosavljevic,
Michael J. Walter
Abstract:
When diamond anvil cell (DAC) sample chambers are outfitted with both thermal insulation and electrodes, two cutting-edge experimental methods are enabled: Joule heating with spectroradiometric temperature measurement, and electrical resistance measurements of samples heated to thousands of kelvin. The accuracy of temperature and resistance measurements, however, often suffers from poor control of…
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When diamond anvil cell (DAC) sample chambers are outfitted with both thermal insulation and electrodes, two cutting-edge experimental methods are enabled: Joule heating with spectroradiometric temperature measurement, and electrical resistance measurements of samples heated to thousands of kelvin. The accuracy of temperature and resistance measurements, however, often suffers from poor control of the shape and location of the sample, electrodes, and thermal insulation. Here, we present a recipe for the reproducible and precise fabrication of DAC sample, electrodes, and thermal insulation using a three-layer microassembly. The microassembly contains two potassium chloride thermal insulation layers, four electrical leads, a sample, and a buttressing layer made of polycrystalline alumina. The sample, innermost electrodes, and buttress layer are fabricated by focused-ion-beam milling. Three iron samples are presented as proof of concept. Each is successfully compressed and pulsed Joule heated while maintaining a four-point probe configuration. The highest pressure-temperature condition achieved is $\sim 150$ GPa and $\sim 4000$ K.
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Submitted 27 October, 2023;
originally announced October 2023.
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Spectroradiometry with sub-microsecond time resolution using multianode photomultiplier tube assemblies
Authors:
Zachary M. Geballe,
Francesca Miozzi,
Chris F. Anto,
Javier Rojas,
Jing Yang,
Michael J. Walter
Abstract:
Accurate and precise measurements of spectroradiometric temperature are crucial for many high pressure experiments that use diamond anvil cells or shock waves. In experiments with sub-millisecond timescales, specialized detectors such as streak cameras or photomultiplier tubes are required to measure temperature. High accuracy and precision are difficult to attain, especially at temperatures below…
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Accurate and precise measurements of spectroradiometric temperature are crucial for many high pressure experiments that use diamond anvil cells or shock waves. In experiments with sub-millisecond timescales, specialized detectors such as streak cameras or photomultiplier tubes are required to measure temperature. High accuracy and precision are difficult to attain, especially at temperatures below 3000 K. Here we present a new spectroradiometry system based on multianode photomultiplier tube technology and passive readout circuitry that yields a 0.24 $μ$s rise-time for each channel. Temperature is measured using five color spectroradiometry. During high pressure pulsed Joule heating experiments in a diamond anvil cell, we document measurement precision to be $\pm 30$ K at temperatures as low as 2000 K during single-shot heating experiments with $0.6$ $μ$s time-resolution. Ambient pressure melting tests using pulsed Joule heating indicate that the accuracy is $\pm 80$ K in the temperature range 1800-2700 K.
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Submitted 25 October, 2023;
originally announced October 2023.
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A broadband pulse amplifier for Joule heating experiments in diamond anvil cells
Authors:
Zachary M. Geballe,
Joseph Lai,
Michael J. Walter
Abstract:
Decades of measurements of the thermophysical properties of hot metals show that pulsed Joule heating is an effective method to heat solid and liquid metals that are chemically reactive or difficult to contain. In order to extend such measurements to megabar pressures, pulsed heating methods must be integrated with diamond anvil cells. We report the design and characterization of a new pulse ampli…
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Decades of measurements of the thermophysical properties of hot metals show that pulsed Joule heating is an effective method to heat solid and liquid metals that are chemically reactive or difficult to contain. In order to extend such measurements to megabar pressures, pulsed heating methods must be integrated with diamond anvil cells. We report the design and characterization of a new pulse amplifier that can heat $\sim 5$ to $50$ $μ$m-diameter metal wires to 1000s of kelvin at megabar pressures using diamond anvil cells. Pulse durations and peak currents can each be varied over 3 orders of magnitude, from 5 $μ$s to 10 ms and 0.2 to 200 A. The pulse amplifier is integrated with a current probe. Two voltage probes attached to the body of a diamond anvil cell can be used to measure voltage in a four point probe geometry. The accuracy of four point probe resistance measurements for a dummy sample with 0.1 $Ω$ resistance are typically better than $5 \%$ at all times from 2 $μ$s to 10 ms after the beginning of the pulse.
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Submitted 30 October, 2023; v1 submitted 23 October, 2023;
originally announced October 2023.
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Fast shimming algorithm based on Bayesian optimization for magnetic resonance based dark matter search
Authors:
Julian Walter,
Hendrik Bekker,
John Blanchard,
Dmitry Budker,
Nataniel L. Figueroa,
Arne Wickenbrock,
Yuzhe Zhang,
Pengyu Zhou
Abstract:
The sensitivity and accessible mass range of magnetic resonance searches for axionlike dark matter depends on the homogeneity of applied magnetic fields. Optimizing homogeneity through shimming requires exploring a large parameter space which can be prohibitively time consuming. We have automated the process of tuning the shim-coil currents by employing an algorithm based on Bayesian optimization.…
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The sensitivity and accessible mass range of magnetic resonance searches for axionlike dark matter depends on the homogeneity of applied magnetic fields. Optimizing homogeneity through shimming requires exploring a large parameter space which can be prohibitively time consuming. We have automated the process of tuning the shim-coil currents by employing an algorithm based on Bayesian optimization. This method is especially suited for applications where the duration of a single optimization step prohibits exploring the parameter space extensively or when there is no prior information on the optimal operation point. Using the Cosmic Axion Spin Precession Experiment (CASPEr)-gradient low-field apparatus, we show that for our setup this method converges after approximately 30 iterations to a sub-10 parts-per-million field homogeneity which is desirable for our dark matter search.
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Submitted 20 September, 2023;
originally announced September 2023.
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Button Shear Testing for Adhesion Measurements of 2D Materials
Authors:
Josef Schätz,
Navin Nayi,
Jonas Weber,
Christoph Metzke,
Sebastian Lukas,
Agata Piacentini,
Eros Reato,
Jürgen Walter,
Tim Schaffus,
Fabian Streb,
Annika Grundmann,
Holger Kalisch,
Michael Heuken,
Andrei Vescan,
Stephan Pindl,
Max C. Lemme
Abstract:
Two-dimensional (2D) materials are considered for numerous applications in microelectronics, although several challenges remain when integrating them into functional devices. Weak adhesion is one of them, caused by their chemical inertness. Quantifying the adhesion of 2D materials on three-dimensional surfaces is, therefore, an essential step toward reliable 2D device integration. To this end, but…
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Two-dimensional (2D) materials are considered for numerous applications in microelectronics, although several challenges remain when integrating them into functional devices. Weak adhesion is one of them, caused by their chemical inertness. Quantifying the adhesion of 2D materials on three-dimensional surfaces is, therefore, an essential step toward reliable 2D device integration. To this end, button shear testing is proposed and demonstrated as a method for evaluating the adhesion of 2D materials with the examples of graphene and hexagonal boron nitride (hBN), molybdenum disulfide, and tungsten diselenide on silicon dioxide (SiO${_2}$) and silicon nitride substrates. We propose a fabrication process flow for polymer buttons on the 2D materials and establish suitable button dimensions and testing shear speeds. We show with our quantitative data that low substrate roughness and oxygen plasma treatments on the substrates before 2D material transfer result in higher shear strengths. Thermal annealing increases the adhesion of hBN on SiO${_2}$ and correlates with the thermal interface resistance between these materials. This establishes button shear testing as a reliable and repeatable method for quantifying adhesion of 2D materials.
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Submitted 13 March, 2024; v1 submitted 11 September, 2023;
originally announced September 2023.
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Signature of (anti)cooperativity in the stochastic fluctuations of small systems: application to the bacterial flagellar motor
Authors:
María-José Franco-Oñate,
Andrea Parmeggiani,
Jérôme Dorignac,
Frédéric Geniet,
Jean-Charles Walter,
Francesco Pedaci,
Ashley L Nord,
John Palmeri,
Nils-Ole Walliser
Abstract:
The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and the residence time in an occupancy state. Since the relative standard deviation from the statistical mean monotonically decreases with the number of binding si…
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The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and the residence time in an occupancy state. Since the relative standard deviation from the statistical mean monotonically decreases with the number of binding sites, these techniques are only suitable for small enough systems, such as those implicated in stochastic processes inside cells. Here, we present a general-purpose grand canonical Hamiltonian description of a small one-dimensional (1D) lattice gas with either nearest-neighbor or long-range interactions as prototypical examples of cooperativity-influenced adsorption processes. First, we elucidate how the strength and sign of the interaction potential between neighboring bound particles on the lattice determine the intensity of the fluctuations of the mean occupancy. We then employ this relationship to compare the theoretical predictions of our model to data from single molecule experiments on bacterial flagellar motors (BFM) of E. coli. In this way, we find evidence that cooperativity controls the mechano-sensitive dynamical assembly of the torque-generating units, the so-called stator units, onto the BFM. Furthermore, in an attempt to quantify fluctuations and the adaptability of the BFM, we estimate the stator-stator interaction potential. Finally, we conclude that the system resides in a sweet spot of the parameter space (phase diagram) suitable for a smoothly adaptive system while minimizing fluctuations.
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Submitted 21 February, 2024; v1 submitted 2 July, 2023;
originally announced July 2023.
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High Density Fabrication Process for Single Flux Quantum Circuits
Authors:
D. Yohannes,
M. Renzullo,
J. Vivalda,
A. C. Jacobs,
M. Yu,
J. Walter,
A. F. Kirichenko,
I. V. Vernik,
O. A. Mukhanov
Abstract:
We implemented, optimized and fully tested over multiple runs a superconducting Josephson junction fabrication process tailored for the integrated digital circuits that are used for control and readout of superconducting qubits operating at millikelvin temperatures. This process was optimized for highly energy efficient single flux quantum (ERSFQ) circuits with the critical currents reduced by fac…
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We implemented, optimized and fully tested over multiple runs a superconducting Josephson junction fabrication process tailored for the integrated digital circuits that are used for control and readout of superconducting qubits operating at millikelvin temperatures. This process was optimized for highly energy efficient single flux quantum (ERSFQ) circuits with the critical currents reduced by factor of ~10 as compared to those operated at 4.2 K. Specifically, it implemented Josephson junctions with 10 uA unit critical current fabricated with a 10 uA/um2 critical current density. In order to circumvent the substantial size increase of the SFQ circuit inductors, we employed a NbN high kinetic inductance layer (HKIL) with a 8.5 pH/sq sheet inductance. Similarly, to maintain the small size of junction resistive shunts, we used a non-superconducting PdAu alloy with a 4.0 ohm/sq sheet resistance. For integration with quantum circuits in a multi-chip module, 5 and 10 um height bump processes were also optimized. To keep the fabrication process in check, we developed and thoroughly tested a comprehensive Process Control Monitor chip set.
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Submitted 18 June, 2023; v1 submitted 12 May, 2023;
originally announced May 2023.
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Physical modeling of ribosomes along messenger RNA: estimating kinetic parameters from ribosome profiling experiments using a ballistic model
Authors:
Carole Chevalier,
Jérôme Dorignac,
Yahaya Ibrahim,
Armelle Choquet,
Alexandre David,
Julie Ripoll,
Eric Rivals,
Frédéric Geniet,
Nils-Ole Walliser,
John Palmeri,
Andrea Parmeggiani,
Jean-Charles Walter
Abstract:
Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume…
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Gene expression consists in the synthesis of proteins from the information encoded on DNA. One of the two main steps of gene expression is the translation of messenger RNA (mRNA) into polypeptide sequences of amino acids. Here, by taking into account mRNA degradation, we model the motion of ribosomes along mRNA with a ballistic model where particles advance along a filament without excluded volume interactions. Unidirectional models of transport have previously been used to fit the average density of ribosomes obtained by the experimental ribo-sequencing (Ribo-seq) technique. In this case an inverse fit gives access to the kinetic rates: the position-dependent speeds and the entry rate of ribosomes onto mRNA. The degradation rate is not, however, accounted for and experimental data from different experiments are needed to have enough parameters for the fit. Here, we propose an entirely novel experimental setup and theoretical framework consisting in splitting the mRNAs into categories depending on the number of ribosomes from one to four. We solve analytically the ballistic model for a fixed number of ribosomes per mRNA, study the different regimes of degradation, and propose a criteria for the quality of the inverse fit. The proposed method provides a high sensitivity to the mRNA degradation rate. The additional equations coming from using the monosome (single ribosome) and polysome (arbitrary number) ribo-seq profiles enable us to determine all the kinetic rates in terms of the experimentally accessible mRNA degradation rate.
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Submitted 26 August, 2022;
originally announced August 2022.
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Replicating analyses of item response curves using data from the Force and Motion Conceptual Evaluation
Authors:
Connor J. Richardson,
Trevor I. Smith,
Paul J. Walter
Abstract:
Ishimoto, Davenport, and Wittmann have previously reported analyses of data from student responses to the Force and Motion Conceptual Evaluation (FMCE), in which they used item response curves (IRCs) to make claims about American and Japanese students' relative likelihood to choose certain incorrect responses to some questions. We have used an independent data set of over 6,500 American students'…
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Ishimoto, Davenport, and Wittmann have previously reported analyses of data from student responses to the Force and Motion Conceptual Evaluation (FMCE), in which they used item response curves (IRCs) to make claims about American and Japanese students' relative likelihood to choose certain incorrect responses to some questions. We have used an independent data set of over 6,500 American students' responses to the FMCE to generate IRCs to test their claims. Converting the IRCs to vectors, we used dot product analysis to compare each response item quantitatively. For most questions, our analyses are consistent with Ishimoto, Davenport, and Wittmann, with some results suggesting more minor differences between American and Japanese students than previously reported. We also highlight the pedagogical advantages of using IRCs to determine the differences in response patterns for different populations to better understand student thinking prior to instruction.
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Submitted 17 April, 2021;
originally announced April 2021.
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Modelling the effect of ribosome mobility on the rate of protein synthesis
Authors:
Olivier Dauloudet,
Izaak Neri,
Jean-Charles Walter,
Jérôme Dorignac,
Frédéric Geniet,
Andrea Parmeggiani
Abstract:
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and th…
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Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation. In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a Totally Asymmetric Simple Exclusion Process (TASEP) coupled to a finite diffusive reservoir, which we call the Ribosome Transport model with Diffusion (RTD). In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion in biological cells is fast enough so that it does not play a role in controlling the rate of translation initiation.
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Submitted 17 January, 2022; v1 submitted 30 September, 2020;
originally announced September 2020.
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Hydrodynamic simulations of sedimenting dilute particle suspensions under repulsive DLVO interactions
Authors:
David Jung,
Maximilian Johannes Uttinger,
Paolo Malgaretti,
Wolfgang Peukert,
Johannes Walter,
Jens Harting
Abstract:
We present guidelines to estimate the effect of electrostatic repulsion in sedimenting dilute particle suspensions. Our results are based on combined Langevin dynamics and lattice Boltzmann simulations for a range of particle radii, Debye lengths and particle concentrations. They show a simple relationship between the slope $K$ of the concentration-dependent sedimentation velocity and the range…
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We present guidelines to estimate the effect of electrostatic repulsion in sedimenting dilute particle suspensions. Our results are based on combined Langevin dynamics and lattice Boltzmann simulations for a range of particle radii, Debye lengths and particle concentrations. They show a simple relationship between the slope $K$ of the concentration-dependent sedimentation velocity and the range $χ$ of the electrostatic repulsion normalized by the average particle-particle distance. When $χ\to 0$, the particles are too far away from each other to interact electrostatically and $K=6.55$ as predicted by the theory of Batchelor. As $χ$ increases, $K$ likewise increases as if the particle radius increased in proportion to $χ$ up to a maximum around $χ=0.4$. Over the range $χ=0.4-1$, $K$ relaxes exponentially to a concentration-dependent constant consistent with known results for ordered particle distributions. Meanwhile the radial distribution function transitions from a disordered gas-like to a liquid-like form. Power law fits to the concentration-dependent sedimentation velocity similarly yield a simple master curve for the exponent as a function of $χ$, with a step-like transition from 1 to 1/3 centered around $χ= 0.6$.
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Submitted 25 February, 2022; v1 submitted 14 August, 2020;
originally announced August 2020.
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Modeling supercoiled DNA interacting with an anchored cluster of proteins: towards a quantitative estimation of chromosomal DNA supercoiling
Authors:
Jean-Charles Walter,
Thibaut Lepage,
Jérôme Dorignac,
Frédéric Geniet,
Andrea Parmeggiani,
John Palmeri,
Jean-Yves Bouet,
Ivan Junier
Abstract:
We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper b…
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We investigate the measurement of DNA supercoiling density ($σ$) along chromosomes using interaction frequencies between DNA and DNA-anchored clusters of proteins. Specifically, we show how the physics of DNA supercoiling leads, in bacteria, to the quantitative modeling of binding properties of ParB proteins around their centromere-like site, {\it parS}. Using this framework, we provide an upper bound for $σ$ in the {\it Escherichia coli} chromosome, consistent with plasmid values, and offer a proof of concept for a high accuracy measurement. To reach these conclusions, we revisit the problem of the formation of ParB clusters. We predict, in particular, that they result from a non-equilibrium, stationary balance between an influx of produced proteins and an outflux of excess proteins, i.e., they behave like liquid-like protein condensates with unconventional ``leaky'' boundaries.
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Submitted 7 April, 2020; v1 submitted 31 January, 2020;
originally announced February 2020.
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Looping and Clustering model for the organization of protein-DNA complexes on the bacterial genome
Authors:
Jean-Charles Walter,
Nils-Ole Walliser,
Gabriel David,
Jérôme Dorignac,
Frédéric Geniet,
John Palmeri,
Andrea Parmeggiani,
Ned S. Wingreen,
Chase P. Broedersz
Abstract:
The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show th…
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The bacterial genome is organized in a structure called the nucleoid by a variety of associated proteins. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the Looping and Clustering (LC) model, which employs a statistical physics approach to describe protein-DNA complexes. The LC model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and the configurational and loop entropy of this protein-DNA cluster. Indeed, we show that the protein interaction strength determines the "tightness" of the loopy protein-DNA complex. With this approach we consider the genomic organization of such a protein-DNA cluster around a single high-affinity binding site. Thus, our model provides a theoretical framework to quantitatively compute the binding profiles of ParB-like proteins around a cognate (parS) binding site.
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Submitted 15 December, 2017; v1 submitted 30 June, 2017;
originally announced July 2017.
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Transition Matrices: A Tool to Assess Student Learning and Improve Instruction
Authors:
Gary A. Morris,
Paul J. Walter,
Spencer Skees,
Samantha Schwartz
Abstract:
This paper introduces a new spreadsheet tool for adoption by high school or college level physics teachers who use common assessments in a pre-instruction/post-instruction mode to diagnose student learning and teaching effectiveness. The spreadsheet creates a simple matrix that identifies the percentage of students who select each possible pre-/post-test answer combination on each question of the…
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This paper introduces a new spreadsheet tool for adoption by high school or college level physics teachers who use common assessments in a pre-instruction/post-instruction mode to diagnose student learning and teaching effectiveness. The spreadsheet creates a simple matrix that identifies the percentage of students who select each possible pre-/post-test answer combination on each question of the diagnostic exam. Leveraging analysis of the quality of the incorrect answer choices, one can order the answer choices from worst to best (i.e., correct), resulting in "transition matrices" that can provide deeper insight into student learning and the success or failure of the pedagogical approach than traditional analyses that employ dichotomous scoring.
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Submitted 12 March, 2017; v1 submitted 5 March, 2017;
originally announced March 2017.
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Compositional evolution during rocky protoplanet accretion
Authors:
Philip J. Carter,
Zoë M. Leinhardt,
Tim Elliott,
Michael J. Walter,
Sarah T. Stewart
Abstract:
The Earth appears non-chondritic in its abundances of refractory lithophile elements, posing a significant problem for our understanding of its formation and evolution. It has been suggested that this non-chondritic composition may be explained by collisional erosion of differentiated planetesimals of originally chondritic composition. In this work, we present N-body simulations of terrestrial pla…
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The Earth appears non-chondritic in its abundances of refractory lithophile elements, posing a significant problem for our understanding of its formation and evolution. It has been suggested that this non-chondritic composition may be explained by collisional erosion of differentiated planetesimals of originally chondritic composition. In this work, we present N-body simulations of terrestrial planet formation that track the growth of planetary embryos from planetesimals. We simulate evolution through the runaway and oligarchic growth phases under the Grand Tack model and in the absence of giant planets. These simulations include a state-of-the-art collision model which allows multiple collision outcomes, such as accretion, erosion, and bouncing events, that enables tracking of the evolving core mass fraction of accreting planetesimals. We show that the embryos grown during this intermediate stage of planet formation exhibit a range of core mass fractions, and that with significant dynamical excitation, enough mantle can be stripped from growing embryos to account for the Earth's non-chondritic Fe/Mg ratio. We also find that there is a large diversity in the composition of remnant planetesimals, with both iron-rich and silicate-rich fragments produced via collisions.
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Submitted 24 September, 2015;
originally announced September 2015.
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A Collisional Origin to Earth's Non-chondritic Composition?
Authors:
Amy Bonsor,
Zoë M. Leinhardt,
Philip J. Carter,
Tim Elliott,
Michael J. Walter,
Sarah T. Stewart
Abstract:
Several lines of evidence indicate a non-chondritic composition for Bulk Earth. If Earth formed from the accretion of chondritic material, its non-chondritic composition, in particular the super-chondritic 142Nd/144Nd and low Mg/Fe ratios, might be explained by the collisional erosion of differentiated planetesimals during its formation. In this work we use an N-body code, that includes a state-of…
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Several lines of evidence indicate a non-chondritic composition for Bulk Earth. If Earth formed from the accretion of chondritic material, its non-chondritic composition, in particular the super-chondritic 142Nd/144Nd and low Mg/Fe ratios, might be explained by the collisional erosion of differentiated planetesimals during its formation. In this work we use an N-body code, that includes a state-of-the-art collision model, to follow the formation of protoplanets, similar to proto-Earth, from differentiated planetesimals (> 100 km) up to isolation mass (> 0.16 M_Earth). Collisions between differentiated bodies have the potential to change the core-mantle ratio of the accreted protoplanets. We show that sufficient mantle material can be stripped from the colliding bodies during runaway and oligarchic growth, such that the final protoplanets could have Mg/Fe and Si/Fe ratios similar to that of bulk Earth, but only if Earth is an extreme case and the core is assumed to contain 10% silicon by mass. This may indicate an important role for collisional differentiation during the giant impact phase if Earth formed from chondritic material.
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Submitted 13 October, 2014;
originally announced October 2014.
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Motor proteins traffic regulation by supply-demand balance of resources
Authors:
Luca Ciandrini,
I. Neri,
Jean-Charles Walter,
O. Dauloudet,
A. Parmeggiani
Abstract:
In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work…
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In cells and in vitro assays the number of motor proteins involved in biological transport processes is far from being unlimited. The cytoskeletal binding sites are in contact with the same finite reservoir of motors (either the cytosol or the flow chamber) and hence compete for recruiting the available motors, potentially depleting the reservoir and affecting cytoskeletal transport. In this work we provide a theoretical framework to study, analytically and numerically, how motor density profiles and crowding along cytoskeletal filaments depend on the competition of motors for their binding sites. We propose two models in which finite processive motor proteins actively advance along cytoskeletal filaments and are continuously exchanged with the motor pool. We first look at homogeneous reservoirs and then examine the effects of free motor diffusion in the surrounding medium. We consider as a reference situation recent in vitro experimental setups of kinesin-8 motors binding and moving along microtubule filaments in a flow chamber. We investigate how the crowding of linear motor proteins moving on a filament can be regulated by the balance between supply (concentration of motor proteins in the flow chamber) and demand (total number of polymerised tubulin heterodimers). We present analytical results for the density profiles of bound motors, the reservoir depletion, and propose novel phase diagrams that present the formation of jams of motor proteins on the filament as a function of two tuneable experimental parameters: the motor protein concentration and the concentration of tubulins polymerized into cytoskeletal filaments. Extensive numerical simulations corroborate the analytical results for parameters in the experimental range and also address the effects of diffusion of motor proteins in the reservoir.
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Submitted 24 September, 2014; v1 submitted 13 August, 2014;
originally announced August 2014.
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Atomistic simulations of electrolyte solutions and hydrogels with explicit solvent models
Authors:
Jonathan Walter,
Stephan Deublein,
Steffen Reiser,
Martin Horsch,
Jadran Vrabec,
Hans Hasse
Abstract:
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the development and optimization of molecular force fields and models, a large number of simulation runs have to be evaluated to obtain the sensitivity of the target pr…
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Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the development and optimization of molecular force fields and models, a large number of simulation runs have to be evaluated to obtain the sensitivity of the target properties with respect to the model parameters. The present work discusses force field development for electrolytes regarding thermodynamic properties of their aqueous solutions. Furthermore, simulations are conducted for the volume transition of hydrogels in the presence of electrolytes. It is shown that the properties of these complex systems can be captured by molecular simulation.
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Submitted 25 July, 2011;
originally announced July 2011.
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Development of models and methods for the molecular simulation of large systems and molecules
Authors:
Jonathan Walter,
Thorsten Merker,
Martin Horsch,
Jadran Vrabec,
Hans Hasse
Abstract:
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new models f…
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The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new models for carbon dioxide and cyclohexanolare discussed and a new method for the model development is introduced. Force fields and models for the simulation of PNIPAAm hydrogel in pure water and sodium chloride solution are tested and verified and applied to the simulation of nucleation processes.
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Submitted 23 May, 2010;
originally announced May 2010.