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At least 307 records · Page 17

Green to red photoconversion of GFP for protein tracking in vivo

A variety of fluorescent proteins have been identified that undergo shifts in spectral emission properties over time or once they are irradiated by ultraviolet or blue light. Such proteins are finding application in following the dynamics of particular proteins or labelled organelles within the cell. However, before genes encoding these fluorescent proteins were available, many proteins have already been labelled with GFP in transgenic cells; a number of model organisms feature collections of GFP-tagged lines and organisms. Here we describe a fast, localized and non-invasive method for GFP photoconversion from green to red. We demonstrate its use in transgenic plant, Drosophila and mammalian cells in vivo. While genes encoding fluorescent proteins specifically designed for photoconversion will usually be advantageous when creating new transgenic lines, our method for photoconversion of GFP allows the use of existing GFP-tagged transgenic lines for studies of dynamic processes in living cells.

Science & Technology - Other Topics↗

First-Principles Calculation of Water p K a Using the Newly Developed SCAN Functional

Acid/base chemistry is an intriguing topic that still constitutes a challenge for computational chemistry. While estimating the acid dissociation constant (or pK a ) could shed light on many chemistry processes, especially in the fields of biochemistry and geochemistry, evaluating the relative stability between protonated and nonprotonated species is often very difficult. Indeed, a prerequisite for calculating the pK a of any molecule is an accurate description of the energetics of water dissociation. In this study, we applied constrained molecular dynamics simulations, a noncanonical sampling technique, to investigate the water deprotonation process by selecting the OH distance as the reaction coordinate. The calculation is based on density functional theory and the newly developed SCAN functional, which has shown excellent performance in describing water structure. This first benchmark of SCAN on a chemical reaction shows that this functional accurately models the energetics of proton transfer reactions in an aqueous environment. After taking Coulomb long-range corrections and nuclear quantum effects into account, the estimated water pK a is only 1.0 pK a unit different from the target experimental value. Our results show that the combination of SCAN and constrained MD successfully reproduces the chemistry of water and constitutes a good framework for calculating the free energy of chemical reactions of interest.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The spin structure of the nucleon

We review the present understanding of the spin structure of protons and neutrons, the fundamental building blocks of nuclei collectively known as nucleons. The field of nucleon spin provides a critical window for testing Quantum Chromodynamics (QCD), the gauge theory of the strong interactions since it involves fundamental aspects of hadron structure, and it can be probed in detail in experiments, particularly deep inelastic lepton scattering on polarized targets. QCD was initially probed in high energy deep inelastic lepton scattering with unpolarized beams and targets. With time, interest shifted from testing perturbative QCD to illuminating the nucleon structure itself. In fact, the spin degrees of freedom of hadrons provides an essential and detailed verification of both perturbative and nonperturbative QCD dynamics. Nucleon spin was initially thought of coming mostly from the spin of its quark constituents, based on intuition from the parton model. However, the first experiments showed that this expectation was incorrect. It is now clear that nucleon physics is much more complex, involving quark orbital angular momenta as well as gluonic and sea quark contributions. Thus, the nucleon spin structure remains a most active aspect of QCD research, involving important advances such as the developments of generalized parton distributions (GPD) and transverse momentum distributions (TMD). Elastic and inelastic lepton-proton scattering, as well as photoabsorption experiments provide various ways to investigate non-perturbative QCD. Fundamental sum rules --such as the Bjorken sum rule for polarized photoabsorption on polarized nucleons-- are also in the non-perturbative domain. This realization triggered a vigorous program to link the low energy effective hadronic description of the strong interactions to fundamental quarks and gluon degrees of freedom of QCD. This has also led to the development of holographic QCD ideas based on the AdS/CFT or gauge/gravity correspondence, a novel approach providing a well-founded semiclassical approximation to QCD. Any QCD-based model of the nucleon's spin and dynamics must also successfully account for the observed spectroscopy of hadrons. Analytic calculations of the hadron spectrum, a long sought goal of QCD research, has now being realized using light-front holography and superconformal quantum mechanics, a formalism consistent with the results from nucleon spin studies. We begin this review with a phenomenological description of nucleon structure in general and of its spin structure in particular, aimed to engage non-specialist readers. A fundamental tool is Dirac's front form and light-front quantization which provides a frame-independent, relativistic description of hadron structure and dynamics, the derivation of spin-sum rules, and a direct connection to the QCD Lagrangian. Next, we discuss the nucleon spin structure at high energy, including topics such as GPDs and TMDs, as well as nucleon spin observables sensitive to final-state interactions such as the Sivers effect. We then discuss experimental and theoretical advances in the nonperturbative domain --in particular the development of light-front holographic QCD and superconformal quantum mechanics, its predictions for the spin content of nucleons, the computation of PDFs and of hadron masses.

74 ATOMIC AND MOLECULAR PHYSICS↗

Uniaxial Compression of Cellular Materials at a 10 -1 s -1 Strain Rate Simultaneously with Synchrotron X-ray Computed Tomographic Imaging

The topic is presented as a series of slides. Motivation for the work included the following: X-ray tomography is a fantastic technique for characterizing a material’s starting structure as well as for non-destructive, in situ experiments to investigate material response; 3D X-ray tomography is needed to fully characterize the morphology of cellular materials; and synchrotron micro-CT can capture 3D images without pausing experiment. Among the conclusions reached are these: High-rate radiographic and tomographic imaging (0.25 s 3D frame rate) using synchrotron CT can capture full 3D images of hyper-elastic materials at a 10 -2 strain rate; dynamic true in situ uniaxial loading can be accurately captured; the three stages of compression can be imaged: bending, buckling, and breaking; implementation of linear modeling is completed; meshes have been imported into LANL modeling codes--testing and validation is underway and direct comparison and validation between in situ data and modeled mechanical response is possible.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

High-Power and Flexible Low-Frequency AC Transmission for Renewable Integration

This project develops a steady-state, dynamic, and production cost models of a multi-terminal, high-power, flexible low-frequency ac (LF-HVac) transmission system with grid-forming converters. Through both numerical analysis and EMTP simulation, the project goal is to demonstrate the feasibility of such an innovative and transformative LF-HVac system to support bulk integration of large-scale, cheap, and steady renewable resources from remote locations such as offshore wind farms to meet recent clean energy goals from DOE. The proposed adoption of low-frequency ac transmission aims to improve power transfer capability for remote large-scale renewable integration. In addition, the control for power electronics converters provides grid-support functions to improve the flexibility and resilience the existing 60-Hz HVac system. Future projects on this topic can be supported by both Energy Efficiency and Renewable Energy (DOEEE) and Office of Electricity Delivery & Energy Reliability (DOEOE) offices.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Three-state majority-vote model on small-world networks

Abstract In this work, we study the opinion dynamics of the three-state majority-vote model on small-world networks of social interactions. In the majority-vote dynamics, an individual adopts the opinion of the majority of its neighbors with probability 1- q , and a different opinion with chance q , where q stands for the noise parameter. The noise q acts as a social temperature, inducing dissent among individual opinions. With probability p , we rewire the connections of the two-dimensional square lattice network, allowing long-range interactions in the society, thus yielding the small-world property present in many different real-world systems. We investigate the degree distribution, average clustering coefficient and average shortest path length to characterize the topology of the rewired networks of social interactions. By employing Monte Carlo simulations, we investigate the second-order phase transition of the three-state majority-vote dynamics, and obtain the critical noise $$q_c$$ q c , as well as the standard critical exponents $$\beta /\nu$$ β / ν , $$\gamma /\nu$$ γ / ν , and $$1/\nu$$ 1 / ν for several values of the rewiring probability p . We conclude that the rewiring of the lattice enhances the social order in the system and drives the model to different universality classes from that of the three-state majority-vote model in two-dimensional square lattices.

99 GENERAL AND MISCELLANEOUS↗

Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

36 MATERIALS SCIENCE↗

Chemically Enabled CO 2 -Enhanced Oil Recovery in Multi-Porosity, Hydrothermally Altered Carbonates in the Southern Michigan Basin - Task 2 Topical Report

This attachment A is a detailed Topical Report for Task 2 (Advanced Field Characterization and Machine Learning Based Data Integration) under the project "Chemically Enabled CO 2 -Enhanced Oil Recovery in Multi-Porosity, Hydrothermally Altered Carbonates in the Southern Michigan Basin." The overall project activity and finding, including the field pilot testing of CO 2 injection are summarized in the companion Final Technical Report The Advanced Field Characterization and Machine Learning Based Data Integration task (Task 2) involved a systematic geologic characterization of the Trenton-Black River (TBR) play in the SMB which included the development of comprehensive datasets, advanced data analytics, risk assessment, and piggyback field characterization. These activities aimed to address the complex carbonate systems by evaluating the extent of fractures, dolomitization, facies, and reservoir properties with the primary objective of informing the static and dynamic modeling, field injection test, and providing input into the development strategy plan. The task was divided into four subtasks: • Subtask 2.1 – Data compilation, review, and analysis • Subtask 2.2 – Risk Assessment • Subtask 2.3 – Advanced Field Characterization • Subtask 2.4 – Integrated Physics-Based Machine Learning and Advanced Data Analytics

02 PETROLEUM↗

Theoretical approach to resonant inelastic x-ray scattering in iron-based superconductors at the energy scale of the superconducting gap

We develop a phenomenological theory to predict the characteristic features of the momentum-dependent scattering amplitude in resonant inelastic x-ray scattering (RIXS) at the energy scale of the superconducting gap in iron-based super-conductors. Taking into account all relevant orbital states as well as their specific content along the Fermi surface we evaluate the charge and spin dynamical structure factors for the compounds LaOFeAs and LiFeAs, based on tight-binding models which are fully consistent with recent angle-resolved photoemission spectroscopy (ARPES) data. We find a characteristic intensity redistribution between charge and spin dynamical structure factors which discriminates between sign-reversing and sign-preserving quasiparticle excitations. Consequently, our results show that RIXS spectra can distinguish between s± and s++ wave gap functions in the singlet pairing case. In addition, we find that an analogous intensity redistribution at small momenta can reveal the presence of a chiral p-wave triplet pairing.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Probing the self-ionization of liquid water with ab initio deep potential molecular dynamics

The chemical equilibrium between self-ionized and molecular water dictates the acid–base chemistry in aqueous solutions, yet understanding the microscopic mechanisms of water self-ionization remains experimentally and computationally challenging. Herein, Density Functional Theory (DFT)–based deep neural network (DNN) potentials are combined with enhanced sampling techniques and a global acid–base collective variable to perform extensive atomistic simulations of water self-ionization for model systems of increasing size. The explicit inclusion of long-range electrostatic interactions in the DNN potential is found to be crucial to accurately reproduce the DFT free energy profile of solvated water ion pairs in small (64 and 128 H 2 O) cells. The reversible work to separate the hydroxide and hydronium to a distance S is found to converge for simulation cells containing more than 500 H 2 O, and a distance of ∼ 8 Å is the threshold beyond which the work to further separate the two ions becomes approximately zero. The slow convergence of the potential of mean force with system size is related to a restructuring of water and an increase of the local order around the water ions. Calculation of the dissociation equilibrium constant illustrates the key role of long-range electrostatics and entropic effects in the water autoionization process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Long‐Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires

Abstract The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano‐ and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein‐protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.

Chemistry↗

Nonequilibrium Aspects of Integrable Models

Driven by breakthroughs in experimental and theoretical techniques, the study of nonequilibrium quantum physics is a rapidly expanding field with many exciting new developments. Among the manifold ways the topic can be investigated, one-dimensional systems provide a particularly fine platform. The trifecta of strongly correlated physics, powerful theoretical techniques, and experimental viability have resulted in a flurry of research activity over the past decade or so. In this review, we explore the nonequilibrium aspects of one-dimensional systems that are integrable. Through a number of illustrative examples, we discuss nonequilibrium phenomena that arise in such models, the role played by integrability, and the consequences these have for more generic systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Physics Opportunities with the 12 GeV Upgrade at Jefferson Lab

We are at the dawn of a new era in the study of hadronic nuclear physics. The non-Abelian nature of Quantum Chromodynamics (QCD) and the resulting strong coupling at low energies represent a significant challenge to nuclear and particle physicists. The last decade has seen the development of new theoretical and experimental tools to quantitatively study the nature of confinement and the structure of hadrons comprised of light quarks and gluons. Together these will allow both the spectrum and the structure of hadrons to be elucidated in unprecedented detail. Exotic mesons that result from excitation of the gluon field will be explored. Multidimensional images of hadrons with great promise to reveal the dynamics of the key underlying degrees of freedom will be produced. In particular, these multidimensional distributions open a new window on the elusive spin content of the nucleon through observables that are directly related to the orbital angular momenta of quarks and gluons. Moreover, computational techniques in Lattice QCD now promise to provide insightful and quantitative predictions that can be meaningfully confronted with, and elucidated by, forthcoming experimental data. In addition, the development of extremely high intensity, highly polarized and extraordinarily stable beams of electrons provides innovative opportunities for probing (and extending) the Standard Model, both through parity violation studies and searches for new particles. Thus the 12 GeV upgrade of the Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Lab will enable a new experimental program with substantial discovery potential to address these and other important topics in nuclear, hadronic and electroweak physics.

43 PARTICLE ACCELERATORS↗

Nuclear Fuel and Pu Redox Studies from The Glenn T. Seaborg Institute at Idaho National Laboratory

The Glenn T. Seaborg Institute at Idaho National Laboratory (INL-GTSI) focuses on advancing fundamental research in the actinide sciences by providing unique opportunities to early career scientists and engineers to gain experience studying the actinide elements and their associated systems. The INL-GTSI is built from three focus areas that are based on the expertise and supporting infrastructure at INL and include solid state chemistry and physics, solution phase chemistry and physics, and forensic and isotope science. INL is the lead Laboratory for nuclear energy research and development in the U. S. and the research on nuclear fuels performed under the INL-GTSI gives good examples of solid state studies. Uranium-Molybdenum (U-Mo) alloys are leading fuel candidates for conversion of high performance research and test reactors to low-enriched fuels. During irradiation, generated fission gas accumulates into bubbles and self-organizes into a gas bubble superlattice (GBS) that effectively stores fission gases and inhibits fuel swelling. A study on the early self- organizing behavior of the GBS shows that not only grain boundaries but the interfaces between the U-Mo matrix and uranium carbide (UC) impurities are important to GBS formation.[1] In solution, understanding the complex redox behavior of plutonium in aqueous environments is critical for establishing optimized nuclear waste reprocessing solvent systems and storage tank environments. INL-GTSI researchers have produced an experimentally validated multi-scale model of the gamma radiation induced behavior of plutonium ions in concentrated aqueous HNO3 solutions.[2] Here, gamma radiation effected only minimal steady state changes in the redox distribution of the plutonium oxidation states. The redox cycling between Pu(IV) and Pu(III) is demonstrated to be mediated by the •OH/NO3• radical oxidation of Pu(III) and the H2O2/HNO3 driven reduction of Pu(IV). The INL-GTSI offers young researchers the unique chance to work directly with actinide bearing materials in a U. S. National Laboratory environment. Further topical areas of interest to the INL-GTSI include, but are not limited to, fundamental actinide properties, structure/property (electronic, magnetic, thermal) relations, actinide quantum criticality, f- electron interactions, electron correlations, computational studies, new phases, defect effects, interface interactions, isotope production and separation, forensic analytical chemistry, structure and dynamic properties of actinides in non-aqueous media, separations chemistry and kinetics for advanced nuclear fuel cycles, radiation effects, and innovative and advanced ligand design for complexation of the actinides.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Physics of Nuclear Collisions at High Energy

A wide range of problems has been investigated in the research program during the period of this grant. Although the major effort has been in the subject of heavy-ion collisions, we have also studied problems in biological and other physical systems. The method of analysis used in reducing complex data in multiparticle production to simple descriptions can also be applied to the study of complex systems of very different nature. Phase transition is an important phenomenon in many areas of physics, and for heavy-ion collisions we study the fluctuations of multiplicities at the critical point. Human brain activities as revealed in EEG also involve fluctuations in time series, and we have found that our experience enables us to find the appropriate quantification of the fluctuations in ways that can differentiate stroke and normal subjects. The main topic that characterizes the research at Oregon in heavy-ion collisions is the recombination model for the treatment of the hadronization process. We have avoided the hydrodynamical model partly because there is already a large community engaged in it, but more significantly we have found the assumption of rapid thermalization unconvincing. Recent results in studying LHC physics lead us to provide more evidence that shower partons are very important even at low p_T, but are ignored by hydro. It is not easy to work in an environment where the conventional wisdom regards our approach as being incorrect because it does not adhere to the standard paradigm. But that is just what a vibrant research community needs: unconventional approach may find evidences that can challenge the orthodoxy. An example is the usual belief that elliptic flow in fluid dynamics gives rise to azimuthal anisotropy. We claim that it is only sufficient but not necessary. With more data from LHC and more independent thinkers working on the subject what is sufficient as a theory may turn out to be incorrect in reality. Another area of investigation that has long been associated with this PI is the study of quark-hadron phase transition in heavy-ion collisions. Finally, at LHC enough particles are produced to make feasible the investigation of intermittency and erraticity indices that we have proposed as signatures of that phase transition.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Effects of electron-phonon interaction on thermal and electrical transport through molecular nano-conductors

The topic of this review is the effects of electron-phonon interaction (EPI) on the transport properties of molecular nano-conductors. A nano-conductor connects to two electron leads and two phonon leads, possibly at different temperatures or chemical potentials. The EPI appears only in the nano-conductor. We focus on its effects on charge and energy transport. We introduce three approaches. For weak EPI, we use the nonequilibrium Green’s function method to treat it perturbatively. We derive the expressions for the charge and heat currents. For weak system-lead couplings, we use the quantum master equation approach. In both cases, we use a simple single level model to study the effects of EPI on the system’s thermoelectric transport properties. It is also interesting to look at the effect of currents on the dynamics of the phonon system. For this, we derive a semi-classical generalized Langevin equation to describe the nano-conductor’s atomic dynamics, taking the nonequilibrium electron system, as well as the rest of the atomic degrees of freedom as effective baths. We show simple applications of this approach to the problem of energy transfer between electrons and phonons.

36 MATERIALS SCIENCE↗

Strain-controlled thermal conductivity in ferroic twinned films

Large reversible changes of thermal conductivity are induced by mechanical stress, and the corresponding device is a key element for phononics applications. We show that the thermal conductivity k of ferroic twinned thin films can be reversibly controlled by strain. Nonequilibrium molecular dynamics simulations reveal that thermal conductivity decreases linearly with the number of twin boundaries perpendicular to the direction of heat flow. Our demonstration of large and reversible changes in thermal conductivity driven by strain may inspire the design of controllable thermal switches for thermal logic gates and all-solid-state cooling devices.

SURFACES, INTERFACES AND THIN FILMS↗

De novo design of drug-binding proteins with predictable binding energy and specificity

The de novo design of small molecule–binding proteins has seen exciting recent progress; however, high-affinity binding and tunable specificity typically require laborious screening and optimization after computational design. We developed a computational procedure to design a protein that recognizes a common pharmacophore in a series of poly(ADP-ribose) polymerase–1 inhibitors. One of three designed proteins bound different inhibitors with affinities ranging from <5 nM to low micromolar. X-ray crystal structures confirmed the accuracy of the designed protein-drug interactions. Molecular dynamics simulations informed the role of water in binding. Binding free energy calculations performed directly on the designed models were in excellent agreement with the experimentally measured affinities. We conclude that de novo design of high-affinity small molecule–binding proteins with tuned interaction energies is feasible entirely from computation.

Science & Technology - Other Topics↗