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At least 325 records · Page 18
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The Role of Hydrophobic Nodes in the Dynamics of Class A β-Lactamases

Class A β-lactamases are known for being able to rapidly gain broad spectrum catalytic efficiency against most β-lactamase inhibitor combinations as a result of elusively minor point mutations. The evolution in class A β-lactamases occurs through optimisation of their dynamic phenotypes at different timescales. At long-timescales, certain conformations are more catalytically permissive than others while at the short timescales, fine-grained optimisation of free energy barriers can improve efficiency in ligand processing by the active site. Free energy barriers, which define all coordinated movements, depend on the flexibility of the secondary structural elements. The most highly conserved residues in class A β-lactamases are hydrophobic nodes that stabilize the core. To assess how the stable hydrophobic core is linked to the structural dynamics of the active site, we carried out adaptively sampled molecular dynamics (MD) simulations in four representative class A β-lactamases (KPC-2, SME-1, TEM-1, and SHV-1). Using Markov State Models (MSM) and unsupervised deep learning, we show that the dynamics of the hydrophobic nodes is used as a metastable relay of kinetic information within the core and is coupled with the catalytically permissive conformation of the active site environment. Finally, our results collectively demonstrate that the class A enzymes described here, share several important dynamic similarities and the hydrophobic nodes comprise of an informative set of dynamic variables in representative class A β-lactamases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

How to Obtain the Redshift Distribution from Probabilistic Redshift Estimates

Abstract A reliable estimate of the redshift distribution n ( z ) is crucial for using weak gravitational lensing and large-scale structures of galaxy catalogs to study cosmology. Spectroscopic redshifts for the dim and numerous galaxies of next-generation weak-lensing surveys are expected to be unavailable, making photometric redshift (photo- z ) probability density functions (PDFs) the next best alternative for comprehensively encapsulating the nontrivial systematics affecting photo- z point estimation. The established stacked estimator of n ( z ) avoids reducing photo- z PDFs to point estimates but yields a systematically biased estimate of n ( z ) that worsens with a decreasing signal-to-noise ratio, the very regime where photo- z PDFs are most necessary. We introduce Cosmological Hierarchical Inference with Probabilistic Photometric Redshifts ( CHIPPR ), a statistically rigorous probabilistic graphical model of redshift-dependent photometry that correctly propagates the redshift uncertainty information beyond the best-fit estimator of n ( z ) produced by traditional procedures and is provably the only self-consistent way to recover n ( z ) from photo- z PDFs. We present the chippr prototype code, noting that the mathematically justifiable approach incurs computational cost. The CHIPPR approach is applicable to any one-point statistic of any random variable, provided the prior probability density used to produce the posteriors is explicitly known; if the prior is implicit, as may be the case for popular photo- z techniques, then the resulting posterior PDFs cannot be used for scientific inference. We therefore recommend that the photo- z community focus on developing methodologies that enable the recovery of photo- z likelihoods with support over all redshifts, either directly or via a known prior probability density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Gating interactions steer loop conformational changes in the active site of the L1 metallo-β-lactamase

β-Lactam antibiotics are the most important and widely used antibacterial agents across the world. However, the widespread dissemination of β-lactamases among pathogenic bacteria limits the efficacy of β-lactam antibiotics. This has created a major public health crisis. The use of β-lactamase inhibitors has proven useful in restoring the activity of β-lactam antibiotics, yet, effective clinically approved inhibitors against class B metallo-β-lactamases are not available. L1, a class B3 enzyme expressed by Stenotrophomonas maltophilia , is a significant contributor to the β-lactam resistance displayed by this opportunistic pathogen. Structurally, L1 is a tetramer with two elongated loops, α3-β7 and β12-α5, present around the active site of each monomer. Residues in these two loops influence substrate/inhibitor binding. To study how the conformational changes of the elongated loops affect the active site in each monomer, enhanced sampling molecular dynamics simulations were performed, Markov State Models were built, and convolutional variational autoencoder-based deep learning was applied. The key identified residues (D150a, H151, P225, Y227, and R236) were mutated and the activity of the generated L1 variants was evaluated in cell-based experiments. The results demonstrate that there are extremely significant gating interactions between α3-β7 and β12-α5 loops. Taken together, the gating interactions with the conformational changes of the key residues play an important role in the structural remodeling of the active site. These observations offer insights into the potential for novel drug development exploiting these gating interactions.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1975

On the control, stability, and waiting time in a slotted ALOHA random-access system

This paper explores some of the boundaries in performance of slotted ALOHA systems by analyzing a simple and almost optimal centrally supervised control. The control results in a very simple Markov chain model and allows an examination of stability, conditional waiting time distribution of transmitting terminals, and many other system measures. The key to the simplicity is to have a probability of successful packet transmission that is independent of the number of transmitting terminals. In considering waiting time, we calculate the mean and other moments of the waiting time of a terminal when it enters the system to find (n - 1) other terminals already there competing for the channel. Under this control, the average time is proportional to n. The control requires exact knowledge of the number of terminals contending for the channel, and hence is not implementable, except as an approximation.

Ferguson, M. J.↗
NASA NTRS1976

Neural pulse frequency modulation of an exponentially correlated Gaussian process

The effect of NPFM (Neural Pulse Frequency Modulation) on a stationary Gaussian input, namely an exponentially correlated Gaussian input, is investigated with special emphasis on the determination of the average number of pulses in unit time, known also as the average frequency of pulse occurrence. For some classes of stationary input processes where the formulation of the appropriate multidimensional Markov diffusion model of the input-plus-NPFM system is possible, the average impulse frequency may be obtained by a generalization of the approach adopted. The results are approximate and numerical, but are in close agreement with Monte Carlo computer simulation results.

Hutchinson, C. E.↗
NASA NTRS1977

Analysis of a first order phase locked loop in the presence of Gaussian noise

A first-order digital phase locked loop is analyzed by application of a Markov chain model. Steady state loop error probabilities, phase standard deviation, and mean loop transient times are determined for various input signal to noise ratios. Results for direct loop simulation are presented for comparison.

Blasche, P. R.↗
NASA NTRS1981

Investigation of air transportation technology at Ohio University, 1980

Specific configurations of first and second order all digital phase locked loops were analyzed for both ideal and additive gaussian noise inputs. In addition, a design for a hardware digital phase locked loop capable of either first or second order operation was evaluated along with appropriate experimental data obtained from testing of the hardware loop. All parameters chosen for the analysis and the design of the digital phase locked loop were consistent with an application to an Omega navigation receiver although neither the analysis nor the design are limited to this application. For all cases tested, the experimental data showed close agreement with the analytical results indicating that the Markov chain model for first and second order digital phase locked loops are valid.

Mcfarland, R. H.↗
NASA NTRS1982

On the delay analysis of a TDMA channel with finite buffer capacity

The throughput performance of a TDMA channel with finite buffer capacity for transmitting data messages is considered. Each station has limited message buffer capacity and has Poisson message arrivals. Message arrivals will be blocked if the buffers are congested. Using the embedded Markov chain model, the solution procedure for the limiting system-size probabilities is presented in a recursive fashion. Numerical examples are given to demonstrate the tradeoffs between the blocking probabilities and the buffer sizing strategy.

Yan, T.-Y.↗
NASA NTRS1982

Reliability calculation using randomization for Markovian fault-tolerant computing systems

The randomization technique for computing transient probabilities of Markov processes is presented. The technique is applied to a Markov process model of a simplified fault tolerant computer system for illustrative purposes. It is applicable to much larger and more complex models. Transient state probabilities are computed, from which reliabilities are derived. An accelerated version of the randomization algorithm is developed which exploits ''stiffness' of the models to gain increased efficiency. A great advantage of the randomization approach is that it easily allows probabilities and reliabilities to be computed to any predetermined accuracy.

Miller, D. R.↗
NASA NTRS1983

Reliability analysis and fault-tolerant system development for a redundant strapdown inertial measurement unit

A methodology is developed and applied for quantitatively analyzing the reliability of a dual, fail-operational redundant strapdown inertial measurement unit (RSDIMU). A Markov evaluation model is defined in terms of the operational states of the RSDIMU to predict system reliability. A 27 state model is defined based upon a candidate redundancy management system which can detect and isolate a spectrum of failure magnitudes. The results of parametric studies are presented which show the effect on reliability of the gyro failure rate, both the gyro and accelerometer failure rates together, false alarms, probability of failure detection, probability of failure isolation, and probability of damage effects and mission time. A technique is developed and evaluated for generating dynamic thresholds for detecting and isolating failures of the dual, separated IMU. Special emphasis is given to the detection of multiple, nonconcurrent failures. Digital simulation time histories are presented which show the thresholds obtained and their effectiveness in detecting and isolating sensor failures.

Motyka, P.↗
NASA NTRS1983

The reliability analysis of a separated, dual fail operational redundant strapdown IMU

A methodology for quantitatively analyzing the reliability of redundant avionics systems, in general, and the dual, separated Redundant Strapdown Inertial Measurement Unit (RSDIMU), in particular, is presented. The RSDIMU is described and a candidate failure detection and isolation system presented. A Markov reliability model is employed. The operational states of the system are defined and the single-step state transition diagrams discussed. Graphical results, showing the impact of major system parameters on the reliability of the RSDIMU system, are presented and discussed.

Motyka, P.↗
NASA NTRS1985

Vector computer memory bank contention

A number of vector supercomputers feature very large memories. Unfortunately the large capacity memory chips that are used in these computers are much slower than the fast central processing unit (CPU) circuitry. As a result, memory bank reservation times (in CPU ticks) are much longer than on previous generations of computers. A consequence of these long reservation times is that memory bank contention is sharply increased, resulting in significantly lowered performance rates. The phenomenon of memory bank contention in vector computers is analyzed using both a Markov chain model and a Monte Carlo simulation program. The results of this analysis indicate that future generations of supercomputers must either employ much faster memory chips or else feature very large numbers of independent memory banks.

Bailey, D. H.↗
NASA NTRS1987

Vector computer memory bank contention

A number of vector supercomputers feature very large memories. Unfortunately the large capacity memory chips that are used in these computers are much slower than the fast central processing unit (CPU) circuitry. As a result, memory bank reservation times (in CPU ticks) are much longer than on previous generations of computers. A consequence of these long reservation times is that memory bank contention is sharply increased, resulting in significantly lowered performance rates. The phenomenon of memory bank contention in vector computers is analyzed using both a Markov chain model and a Monte Carlo simulation program. The results of this analysis indicate that future generations of supercomputers must either employ much faster memory chips or else feature very large numbers of independent memory banks.

Bailey, David H.↗
NASA NTRS1988

Meteorological and Environmental Inputs to Aviation Systems

Reports on aviation meteorology, most of them informal, are presented by representatives of the National Weather Service, the Bracknell (England) Meteorological Office, the NOAA Wave Propagation Lab., the Fleet Numerical Oceanography Center, and the Aircraft Owners and Pilots Association. Additional presentations are included on aircraft/lidar turbulence comparison, lightning detection and locating systems, objective detection and forecasting of clear air turbulence, comparative verification between the Generalized Exponential Markov (GEM) Model and official aviation terminal forecasts, the evaluation of the Prototype Regional Observation and Forecast System (PROFS) mesoscale weather products, and the FAA/MIT Lincoln Lab. Doppler Weather Radar Program.

Camp, Dennis W.↗