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At least 613 records · Page 34

Peptide Hit Results Processor

The Peptide Hit Results Processor (PHRP) can be used to convert an X!Tandem results file (XML format), MSGF+ .tsv search result file, Sequest Synopsis/First Hits file, or Inspect search result into a series of tab-delimited text files summarizing the results. It will insert modification symbols into the peptide sequences for modified peptides. Parallel files are created containing sequence information, modification details, and protein information. The user can optionally provide a modification definition file that specifies the symbol to use for each modification mass.

Gibbons, Bryson↗

Sandia Cloud Forensics and Incident Response Platform v 1.0

As systems and devices become virtualized and deployed in the cloud, the hypervisor becomes an increasingly appropriate place to collect performance data, system state, system landscape, function calls, transaction traces, and other characteristics. We developed a method by which an introspection application may be coupled with a hypervisor to “reach into” the VM with minimal intrusiveness to collect data critical to the reconstruction of events, files, and operations. Such a capability is required to take advantage of the hypervisor as an instrumentation platform and to integrate that data with more traditional collection mechanisms. The concept of a VM serviced by a lightweight hypervisor is a relatively new paradigm for forensic practitioners. Traditional forensic techniques, based on assumptions that the filesystem was directly interacting with the hardware through an abstraction, afforded the forensic practitioner the assumption that there was nothing controlling the application below the filesystem. This is not the case when using virtualized technologies. Hypervisors can covertly monitor, introspect and interact with the guest in a transparent fashion. The problems of storage and collection of actionable data are exhausting. The current challenge is most hypervisors do not expose a useful application programming interface (API) at a sufficient level to do transparent, fine-grained and customizable introspection. Scalable VM instrumentation and introspection at an in-depth level requires fast handling of events, as well as direct access to VM state. Furthermore, deep introspection benefits greatly from the ability to gather data from the hardware during the VM’s exit to the hypervisor. All of this requires identical access to the system as the hypervisor itself; improper use of this ability could easily cause system instability. It is for this reason we believe that the hypervisor developers have been hesitant to grant this much control through their APIs. However, our approach leverages other means to collect and monitor the guests in a targeted fashion. Virtual machine introspection (VMI) is a technique used to monitor the runtime state of a system-level virtual machine. The runtime state can be may include processor registers, memory, disk, network, and any other hardware-level events A review of research literature and current VMI technologies exposed several limitations and tradeoffs in VMI approaches, including: the use of in-guest agents; kernel to user space transitions (dramatically slowing down processing); VMI tool pre-configuration requirements; hypervisor version lock-in or source code patching; reliance on operating system symbols; limited processor features due to hypervisor (even if the hardware could do more). To address these constraints, a VMI tool was envisioned to provide the cloud forensic capabilities while having as few of these limitations as possible. The Kernel-based Virtual Machine Introspection (KVMi) tool was developed for hypervisors on Intel’s x86-64 architecture. To meet performance, scoping and use-case demands, the follow criteria were applied to KVMi to support live, forensic data collection: • Shall not require in-guest agents. • Shall work with any recent version of modern hypervisors. • Shall introspect upon any guest (VM) running modern versions of Windows, Linux and OS X. • Shall have the ability to find and track operating system artifacts • Shall not require operating system symbol files. • Shall be able to fully handle VM-exits, bypassing execution of the hypervisor if necessary, to facilitate new features the hypervisor may not support. • Shall be compilable/loadable on a running system with standard build tools.

Stout, WilliamM.S.↗

DEPRECATED AI-Batt-OS (Autonomous Identification of Battery Life Models - Open Source) [SWR 21-17]

DEPRECATED. This repository was archived by the owner on Jun 30, 2026. It is now read-only. Open source implementation of some of the methods utilized by AI-Batt, a battery lifetime modeling and analysis toolkit provided by the National Laboratory of the Rockies (NLR). This software demonstrates the use of bi-level optimization and symbolic regression techniques to semi-autonomously identify algebraic models predicting the capacity fade of lithium-ion batteries during calendar aging. Modeling the degradation of batteries is a complex task, due to the difficulty in separating the time-dependent and time-independent factors impacting cell level degradation, across multiple data series with different numbers of measurements and/or data quality. Bi-level optimization enables model parameters to be optimized to either the entire data set or to individual data series, allowing statistical disambiguation of global behaviors (data series independent) and local behaviors (data series dependent). Symbolic regression is used to automatically search for optimal low-dimesional models predicting the variation of locally optimized parameters versus time-independent experimental variables from millions of possible models, resulting in a more accurate and repeatable model identification process than is possible by a manual search. The provided tools also implement cross-validation and bootstrap resampling schemes, empowering statistical model comparison/selection and quantification of model uncertainties. An example script replicates the results from the manuscript "Challenging Practices of Algebraic Battery Life Models through Statistical Validation and Model Identification via Machine-Learning", submitted to ECS. All code is written in MATLAB. Requires the Statistics and Machine Learning Toolbox. Contact Dr. Paul Gasper at Paul.Gasper@nlr.gov for any questions.

Gasper, Paul↗

STreCH

Symbolic regression software that formulates a symbolic regression problem as a mixed-integer nonlinear optimization problem, and solves it using a sequential tree construction heuristic

Leyffer, Sven↗

Camellia: A Rapid Development Framework for Finite Element Solvers

We report the discontinuous Petrov–Galerkin (DPG) methodology of Demkowicz and Gopalakrishnan guarantees the optimality of the finite element solution in a user-controllable energy norm, and provides several features supporting adaptive schemes. The approach provides stability automatically; there is no need for carefully derived numerical fluxes (as in DG schemes) or for mesh-dependent stabilization terms (as in stabilized methods). In this paper, we focus on features of Camellia that facilitate implementation of new DPG formulations; chief among these is a rich set of features in support of symbolic manipulation, which allow, e.g., bilinear formulations in the code to appear much as they would on paper. Many of these features are general in the sense that they can also be used in the implementation of other finite element formulations. In fact, because DPG’s requirements are essentially a superset of those of other finite element methods, Camellia provides built-in support for most common methods. We believe, however, that the combination of an essentially “hands-free” finite element methodology as found in DPG with the rapid development features of Camellia are particularly winsome, so we focus on use cases in this class. In addition to the symbolic manipulation features mentioned above, Camellia offers support for one-irregular adaptive meshes in 1D, 2D, 3D, and space-time. It provides a geometric multigrid preconditioner particularly suited for DPG problems, and supports distributed parallel execution using MPI. For its load balancing and distributed data structures, Camellia relies on packages from the Trilinos project, which simplifies interfacing with other computational science packages. Camellia also allows loading of standard mesh formats through an interface with the MOAB package. Camellia includes support for static condensation to eliminate element-interior degrees of freedom locally, usually resulting in substantial reduction of the cost of the global problem. Finally, we include a discussion of the variational formulations built into Camellia, with references to those formulations in the literature, as well as an MPI performance study.

97 MATHEMATICS AND COMPUTING↗

Caltech campus executive LDRD.

The environment most brain systems of humans and other animals are almost constantly confronted with is complex and continuously changing, with each time step updating a potentially bewildering set of opportunities and demands for action. Far from the controlled, discrete trials used in most neuro- and psychological investigations, behavior outside the lab at Caltech is a seamless and continuous process of monitoring (and error correction) of ongoing action, and of evaluating persistence in the current activity with respect to opportunities to switch tasks as alternatives become available. Prior work on frontopolar and prefrontal task switching, use tasks within the same modality (View a stream of symbols on a screen and perform certain response mappings depending on task rules). However, in these task switches the effector is constant: only the mapping of visual symbols to the specific button changes. In this task, the subjects are choosing what kinds of future action decisions they want to perform, where they can control either which body part will act, or which direction they will orient an instructed body action. An effector choice task presents a single target and the subject selects which effector to use to reach the target (eye or hand). While the techniques available for humans can be less spatially resolved compared to non-human primate neural data, they do allow for experimentation on multiple brain areas with relative ease. Thus, we address a broader network of areas involved in motor decisions. We aim to resolve a current dispute regarding the specific functional roles of brain areas that are often co-activated in studies of decision tasks, dorsal premotor cortex(PMd) and posterior parietal cortex(PPC). In one model, the PPC distinctly drives intentions for action selection, whereas PMd stimulation results in complex multi-joint movements without any awareness of, nor subjective feeling of, willing the elicited movement, thus seems to merely help execute the chosen action.

Shepodd, Timothy J.↗

A comparison of different methods to implement higher order derivatives of density functionals

Density functional theory is the dominant approach in electronic structure methods today. To calculate properties higher order derivatives of the density functionals are required. These derivatives might be implemented manually,by automatic differentiation, or by symbolic algebra programs. Different authors have cited different reasons for using the particular method of their choice. This paper presents work where all three approaches were used and the strengths and weaknesses of each approach are considered. It is found that all three methods produce code that is suffficiently performanted for practical applications, despite the fact that our symbolic algebra generated code and our automatic differentiation code still have scope for significant optimization. The automatic differentiation approach is the best option for producing readable and maintainable code.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Quick Guide for SNS-NSE Reduction Software DrSpine (Data Reduction for Spin Echo)

This is a general guide to quick access the most common commands for DrSpine (Data Reduction for Spin Echo) data reduction software of the SNS-NSE spectrometer. Over the length of the manuscript the symbol “ $ “ represents the OS shell prompt, i.e., the beginning of a command line in a shell terminal, while the symbol “-->” represents the beginning of a command line in the DrSpine reduction software, after the activation of the reduction environment.

97 MATHEMATICS AND COMPUTING↗

Automated and Accelerated Continuum Model Development for Electrochemical Systems (Abbreviated Report)

Despite the availability of computational resources and advancements in numerical computing capabilities, the multiscale models core to understanding, predicting the behaviors of, and designing energy and environmental systems involving porous media are still 1.) developed through by-hand derivations and 2.) limited by many methodological assumptions employed during model derivation. As a result, the advancement of effective media models for engineering DOE mission-critical systems (e.g., batteries, flow batteries, electrolyzers, geothermal systems, subsurface chemical storage systems, etc.) is slow (i.e., it takes years for models to traverse from stages of “development” to “practical utilization”), hindering our ability to effectively optimize such systems and stay at the cutting-edge of the energy frontier. In this work, we aimed to address these limitations by 1.) automating and accelerating multiscale model derivation via symbolic computing and 2.) develop a novel multiscale modeling methodology for flow and transport through porous media that avoids the typical assumptions hindering previous models. As a result of our efforts, we 1.) developed a hybrid symbolic-numeric code called Fouriera for fully-automating the implementation of multiphysical and phase-field models via the Fourier spectral method for materials science research, and 2.) advanced a multiscale modeling methodology called The Method of Finite Averages that rigorously predicts the behaviors of flow and transport through heterogeneous porous media under the influence of non-local effects and strong advection. Ultimately, these deliverables provide strong foundations from which further efforts can advance multiscale modeling tools and capabilities that do not intrinsically rely on 1.) the speed and mathematical capabilities of humans, nor 2.) the methodological assumptions limiting current models.

36 MATERIALS SCIENCE↗

Filterbank Multicarrier Communications for High Mobility Underwater Acoustic Links

This paper presents a new method of designing prototype filters that are robust against time and frequency dispersive (i.e., doubly dispersive) underwater acoustic (UWA) channels. The proposed design uses a modified form of Slepian sequences as a basis set to arrive at a design that is maximally compact along both time and frequency/Doppler dimensions. This keeps the inter-symbol interference confined to a small number of adjacent data symbols, both across time and frequency dimensions. It also minimizes the ramp-up (at the beginning) and ramp-down (at the end) of each synthesized data packet. Here, we test our design by making use of the BELLHOP/VirTex channel simulator and compare its performance with that of the widely used orthogonal frequency division multiplexing (OFDM) method. Our emphasis is on scenarios where the channel impulse response extends to a few hundreds of milli-seconds and the relative speed of communicating vehicles can be as large as 10 m/s. We find that while OFDM fails in majority of these scenarios, the proposed design continues to work well in all the scenarios that we simulate.

97 - MATHEMATICS AND COMPUTING↗

Synthesis, Crystal and Electronic Structures of the Pnictides AE 3 TrPn 3 (AE = Sr, Ba; Tr = Al, Ga; Pn = P, As)

New ternary arsenides AE 3 TrAs 3 (AE = Sr, Ba; Tr = Al, Ga) and their phosphide analogs Sr 3 GaP 3 and Ba 3 AlP 3 have been prepared by reactions of the respective elements at high temperatures. Single-crystal X-ray diffraction studies reveal that Sr 3 AlAs 3 and Ba 3 AlAs 3 adopt the Ba 3 AlSb 3 -type structure (Pearson symbol oC56, space group Cmce, Z = 8). This structure is also realized for Sr 3 GaP 3 and Ba 3 AlP 3 . Likewise, the compounds Sr 3 GaAs 3 and Ba 3 GaAs 3 crystallize with the Ba 3 GaSb 3 -type structure (Pearson symbol oP56, space group Pnma, Z = 8). Both structures are made up of isolated pairs of edge-shared AlPn 4 and GaPn 4 tetrahedra (Pn = pnictogen, i.e., P or As), separated by the alkaline-earth Sr 2+ and Ba 2+ cations. In both cases, there are no homoatomic bonds, hence, regardless of the slightly different atomic arrangements, both structures can be rationalized as valence-precise [AE 2+ ] 3 [Tr 3+ ][Pn 3- ] 3 , or rather [AE 2+ ] 6 [Tr 2 Pn 6 ] 12- , i.e., as Zintl phases.

36 MATERIALS SCIENCE↗

Synthesis and Structural Characterization of Ba7Li11Bi10 and AE4(Li,Tr)7Pn6 (AE = Sr, Ba, Eu; Tr = Ga, In; Pn = Sb, Bi)

Reported are the synthesis and crystal structure of Ba7Li11Bi10, a new ternary compound crystallizing in its own type with the monoclinic space group C2/m (a = 18.407(3) Å, b = 5.0258(9) Å, and c = 18.353(3) Å; β = 104.43(1)°; Pearson symbol mS56), and those of the structurally related quaternary phases Ba4(Li1−xGax)7Sb6, Ba4(Li1−xInx)7Sb6, Ba4(Li1−xInx)7Bi6, and Eu4(Li1−xInx)7Bi6 (crystallizing in the Eu4Li7Bi6 structure type with the same monoclinic space group C2/m (a = 18.4045(13)–17.642(4) Å, b = 5.012(4)–4.8297(10) Å, and c = 13.2792(10)–12.850(3) Å, β = 126.80(1)–125.85(1)°; Pearson symbol mS34). All studied compounds are identified among the products of the high-temperature reactions of the corresponding elements. Both types of crystal structures are based on corner- and edge-linked Li-centered Sb4 (or Bi4) tetrahedra, Sb6 (or Bi6) octahedra, and Sb2 or Bi2 dumbbells. Given the similarities between the two structures, it might be proposed that they represent the simplest members of a potentially large homologous series described with the general formulae (BaLi3Sb2)n(Ba3Li4Sb4)m or (BaLi3Bi2)n(Ba3Li4Bi4)m, where the more complicated “7-11-10” phase is the member with n = 2 and m = 1, while the “4-7-6” one is the intergrowth of the two components in an equal ratio. The computed electronic band structures of Ba7Li11Bi10 and idealized Ba4Li7Bi6 (a model for Ba4(Li1−xInx)7Bi6) are also discussed.

Ojwang, Dickson O. (ORCID:0000000193048975)↗

Distribution of mica polytypes among space groups.

All the possible space groups for mica polytypes are deduced by making use of the characteristics of the mica unit layer and stacking mode. The algebraic properties of the vector-stacking symbol of Ross et al. (1966) are examined, and a simple algorithm for deducing the space group from this symbol is presented. A method considered for enumerating all possible stacking sequences of mica polytypes makes use of a computer.

Takeda, H.↗

Terminal context in context-sensitive grammars.

Investigation of the conditions whereunder context-sensitive grammars generate context-free languages. The obtained results indicate that, if every noncontext-free rewriting rule of a context-sensitive grammar has as left context a string of terminal symbols and the left context is at least as long as the right context, then the language generated is context-free. Likewise, if every noncontext-free rewriting rule of a context-sensitive grammar has strings of terminal symbols as left and right contexts, then the language generated is also context-free.

Book, R. V.↗

Multifunction display system

The design and characteristics of a multifunction display system are discussed. The system is a general purpose, time-shared, electro-optical display driven by onboard data management systems. It is capable of presenting information in forms such as alphanumerics, symbolics, and graphics, separately or in combination. The components of the system are: (1) data terminal simulator/input loader, (2) keyboard controller, (3) CRT display indicator, and (4) programmable symbol generator.

Kendall, K.↗

The effectiveness of correcting codes in reception in the whole in additive normal white noise

Some possible criteria for estimating the effectiveness of correcting codes are presented, and the energy effectiveness of correcting codes is studied for symbol-by-symbol reception. Expressions for the energetic effectiveness of binary correcting codes for reception in the whole are produced. Asymptotic energetic effectiveness and finite signal/noise ratio cases are considered.

Shtarkov, Y. M.↗

The DLG processor: A data management executive for the engineering design integration (EDIN) system. Volume 1: Engineering description and utilization manual

The DLG processor is a Univac 1100 series computer program designed to read, modify, manipulate, and replace symbolic images. DLG is controlled by a set of user supplied directives and operates from a data base of stratified information which can be merged with the symbolic images. Data bases can be constructed and maintained in the mass storage media using the DLG directive language.

Glatt, C. R.↗

A conformal head-up display for the visual approach

The degree of conformity used in matching a superimposed display to its visual background is considered in relation to the information available for vertical guidance and control during a purely visual approach. The information may be represented by individual symbols or combined in a single symbol, and the relative merits of these methods are discussed. A fully conformal display format is developed for the purpose of showing both the position and direction of the flight path, with provision for the effects of disturbances, ILS compatibility, and control needs. The field of view needed for all conditions and phases of the visual approach with a fully conformal display is studied in relation to the limitations of conventional collimator systems. Methods are discussed which depend on deviation of the sight line, and on windshield reflection of the uncollimated image of a simple pointer. Limited flight tests show some promise for the uncollimated method.

Naish, J. M.↗