89 research outputs found
Interatomic potentials for mixed oxide (MOX) nuclear fuels
We extend our recently developed interatomic potentials for UO_{2} to the
mixed oxide fuel system (U,Pu,Np)O_{2}. We do so by fitting against an
extensive database of ab initio results as well as to experimental
measurements. The applicability of these interactions to a variety of mixed
environments beyond the fitting domain is also assessed. The employed formalism
makes these potentials applicable across all interatomic distances without the
need for any ambiguous splining to the well-established short-range
Ziegler-Biersack-Littmark universal pair potential. We therefore expect these
to be reliable potentials for carrying out damage simulations (and Molecular
Dynamics simulations in general) in nuclear fuels of varying compositions for
all relevant atomic collision energies
Inferring phase transitions and critical exponents from limited observations with Thermodynamic Maps
Phase transitions are ubiquitous across life, yet hard to quantify and
describe accurately. In this work, we develop an approach for characterizing
generic attributes of phase transitions from very limited observations made
deep within different phases' domains of stability. Our approach is called
Thermodynamic Maps, which combines statistical mechanics and molecular
simulations with score-based generative models. Thermodynamic Maps enable
learning the temperature dependence of arbitrary thermodynamic observables
across a wide range of temperatures. We show its usefulness by calculating
phase transition attributes such as melting temperature, temperature-dependent
heat capacities, and critical exponents. For instance, we demonstrate the
ability of thermodynamic maps to infer the ferromagnetic phase transition of
the Ising model, including temperature-dependent heat capacity and critical
exponents, despite never having seen samples from the transition region. In
addition, we efficiently characterize the temperature-dependent conformational
ensemble and compute melting curves of the two RNA systems GCAA tetraloop and
HIV-TAR, which are notoriously hard to sample due to glassy-like landscapes
Spontaneous Polarization in an Ultrathin Improper-Ferroelectric/Dielectric Bilayer in a Capacitor Structure at Cryogenic Temperatures
To determine the effect of depolarization and the critical thickness in improper-ferroelectric hexagonal-ferrite thin films, we investigate the polarization switching of a ferroelectric/dielectric bilayer in capacitor structures at 20 K. Experimentally, we show that the spontaneous polarization persists throughout the studied thickness range (3 to 80 unit cell), even with a thick (10-nm) dielectric layer, suggesting no practical thickness limit for applications. By fitting the effect of depolarization using the phenomenological theory, we show that the spontaneous polarization remains finite when the thickness of the ferroelectric layer approaches zero, providing a hint for the absence of critical thickness. We also find that the interfacial effects limit the multidomain formation and govern the polarization switching mechanisms
Chikungunya virus infectivity, RNA replication and non-structural polyprotein processing depend on the nsP2 protease's active site cysteine residue
Chikungunya virus (CHIKV), genus Alphavirus, family Togaviridae, has a positive-stand RNA genome approximately 12 kb in length. In infected cells, the genome is translated into non-structural polyprotein P1234, an inactive precursor of the viral replicase, which is activated by cleavages carried out by the non-structural protease, nsP2. We have characterized CHIKV nsP2 using both cell-free and cell-based assays. First, we show that Cys478 residue in the active site of CHIKV nsP2 is indispensable for P1234 processing. Second, the substrate requirements of CHIKV nsP2 are quite similar to those of nsP2 of related Semliki Forest virus (SFV). Third, substitution of Ser482 residue, recently reported to contribute to the protease activity of nsP2, with Ala has almost no negative effect on the protease activity of CHIKV nsP2. Fourth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 completely abolished RNA replication in CHIKV and SFV trans-replication systems. In contrast, trans-replicases with Ser482 to Ala mutation were similar to wild type counterparts. Fifth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 abolished the rescue of infectious virus from CHIKV RNA transcripts while Ser482 to Ala mutation had no effect. Thus, CHIKV nsP2 is a cysteine protease.Peer reviewe
Design and Validation of Novel Chikungunya Virus Protease Inhibitors
Chikungunya virus (CHIKV; genus Alphavirus) is the causative agent of chikungunya fever. CHIKV replication can be inhibited by some broad-spectrum antiviral compounds; in contrast, there is very little information about compounds specifically inhibiting the enzymatic activities of CHIKV replication proteins. These proteins are translated in the form of a nonstructural (ns) P1234 polyprotein precursor from the CHIKV positive-strand RNA genome. Active forms of replicase enzymes are generated using the autoproteolytic activity of nsP2. The available three-dimensional (3D) structure of nsP2 protease has made it a target for in silico drug design; however, there is thus far little evidence that the designed compounds indeed inhibit the protease activity of nsP2 and/or suppress CHIKV replication. In this study, a set of 12 compounds, predicted to interact with the active center of nsP2 protease, was designed using target-based modeling. The majority of these compounds were shown to inhibit the ability of nsP2 to process recombinant protein and synthetic peptide substrates. Furthermore, all compounds found to be active in these cell-free assays also suppressed CHIKV replication in cell culture, the 50% effective concentration (EC50) of the most potent inhibitor being similar to 1.5 mu M. Analysis of stereoisomers of one compound revealed that inhibition of both the nsP2 protease activity and CHIKV replication depended on the conformation of the inhibitor. Combining the data obtained from different assays also indicates that some of the analyzed compounds may suppress CHIKV replication using more than one mechanism.Peer reviewe
Global delivery models: the role of talent, speed and time zones in the global outsourcing industry
Global delivery models (GDMs) are transforming the global IT and business process outsourcing industry. GDMs are a new form of client-specific investment promoting service integration with clients by combining client proximity with time-zone spread for 24/7 service operations. We investigate antecedents and contingencies of setting up GDM structures. Based on comprehensive data we show that providers are likely to establish GDM location configurations when clients value access to globally distributed talent and speed of service delivery, in particular when services are highly commoditized. Findings imply that coordination across time zones increasingly affects international operations in business-to-business and born-global industries
Molecular residual disease detection in resected, muscle-invasive urothelial cancer with a tissue-based comprehensive genomic profiling–informed personalized monitoring assay
IntroductionCirculating tumor DNA (ctDNA) detection postoperatively may identify patients with urothelial cancer at a high risk of relapse. Pragmatic tools building off clinical tumor next-generation sequencing (NGS) platforms could have the potential to increase assay accessibility.MethodsWe evaluated the widely available Foundation Medicine comprehensive genomic profiling (CGP) platform as a source of variants for tracking of ctDNA when analyzing residual samples from IMvigor010 (ClinicalTrials.gov identifier NCT02450331), a randomized adjuvant study comparing atezolizumab with observation after bladder cancer surgery. Current methods often involve germline sampling, which is not always feasible or practical. Rather than performing white blood cell sequencing to filter germline and clonal hematopoiesis (CH) variants, we applied a bioinformatic approach to select tumor (non-germline/CH) variants for molecular residual disease detection. Tissue-informed personalized multiplex polymerase chain reaction–NGS assay was used to detect ctDNA postsurgically (Natera).ResultsAcross 396 analyzed patients, prevalence of potentially actionable alterations was comparable with the expected prevalence in advanced disease (13% FGFR2/3, 20% PIK3CA, 13% ERBB2, and 37% with elevated tumor mutational burden ≥10 mutations/megabase). In the observation arm, 66 of the 184 (36%) ctDNA-positive patients had shorter disease-free survival [DFS; hazard ratio (HR) = 5.77; 95% confidence interval (CI), 3.84–8.67; P < 0.0001] and overall survival (OS; HR = 5.81; 95% CI, 3.41–9.91; P < 0.0001) compared with ctDNA-negative patients. ctDNA-positive patients had improved DFS and OS with atezolizumab compared with those in observation (DFS HR = 0.56; 95% CI, 0.38–0.83; P = 0.003; OS HR = 0.66; 95% CI, 0.42–1.05). Clinical sensitivity and specificity for detection of postsurgical recurrence were 58% (60/103) and 93% (75/81), respectively.ConclusionWe present a personalized ctDNA monitoring assay utilizing tissue-based FoundationOne® CDx CGP, which is a pragmatic and potentially clinically scalable method that can detect low levels of residual ctDNA in patients with resected, muscle-invasive bladder cancer without germline sampling
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