First-principles study of the Pd–Si system and Pd(0 0 1)/SiC(0 0 1) hetero-structure
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The collection and analysis of volatile memory is a vibrant area of research in the cybersecurity community. The ever-evolving and growing threat landscape is trending towards fileless malware, which avoids traditional detection but can be found by examining a system’s random access memory (RAM). Additionally, volatile memory analysis offers great insight into other malicious vectors. It contains fragments of encrypted files’ contents, as well as lists of running processes, imported modules, and network connections, all of which are difficult or impossible to extract from the file system. For these compelling reasons, recent research efforts have focused on the collection of memory snapshots and methods to analyze them for the presence of malware. However, to the best of our knowledge, no current reviews or surveys exist that systematize the research on both memory acquisition and analysis. We fill that gap with this novel survey by exploring the state-of-the-art tools and techniques for volatile memory acquisition and analysis for malware identification. For memory acquisition methods, we explore the trade-offs many techniques make between snapshot quality, performance overhead, and security. For memory analysis, we examined the traditional forensic methods used, including signature-based methods, dynamic methods performed in a sandbox environment, as well as machine learning-based approaches. We summarize the currently available tools, and suggest areas for more research.
During the dissociative adsorption on a solid surface, the substrate usually participates in a passive manner to accommodate fragments produced upon the cleavage of the internal bond(s) of a (transient) molecular adsorbate. This simple picture, however, neglects the flexibility of surface atoms. Here, we report a Density Functional Theory study to revisit our early studies of the dissociative adsorption of CH{sub 3}X (X = Br and Cl) on Si(100). We have identified a new reaction pathway, which involves a flip of a silicon dimer; this new pathway agrees better with experiments. For our main exemplar of CH{sub 3}Br, insights have been gained using a simple model that involves a three-atom reactive center, Br-C-Si. When the silicon dimer flips, the interaction between C and Si in the Br-C-Si center is enhanced, evident in the increased energy-split of the frontier orbitals. We also examine how the dissociation dynamics of CH{sub 3}Br is altered on a heterodimer (Si-Al, Si-P, and Si-Ge) in a Si(100) surface. In each case, we conclude, on the basis of computed reaction pathways, that no heterodimer flipping is involved before the system transverses the transition state to dissociative adsorption.
Multimodal chromatography uses small ligands with multiple modes of interaction, e.g., charged, hydrophobic or hydrogen bonding, to separate proteins from complex mixtures. The mechanism by which multimodal ligands interact with proteins is expected to be affected by ligand conformations, among other factors. In this report, we determine conformational equilibria of two commercially used multimodal cation exchange ligands, Capto MMC and Nuvia cPrime, in a range of solvents, a Lennard-Jones (LJ) liquid, ethanol, and water, using molecular dynamics (MD) simulations. By mapping ligand conformations onto two key torsion angles, ω and φ, in these solvents and in low and high dielectric media, we quantify the relative importance of intramolecular and solvent-mediated interactions. In a high dielectric medium, Capto MMC preferentially samples three conformations, which are stabilized by a combination of an intramolecular torsion potential (on ω) and LJ interactions. In an LJ liquid, solvent molecules compete with intramolecular interactions while simultaneously providing an osmotic force, stabilizing both closer and farther distances between ligand sites. This has the overall result of “flattening out” the conformational landscape. Interestingly, in ethanol and water, hydrogen bonding among the amide hydrogen and solvent molecules stabilizes two additional conformations of Capto MMC in which ω takes on less favorable cis-like configurations. MD simulations of ligands in free solution with three therapeutic antibody fragments show that ligand conformational equilibria remain effectively unchanged upon binding to proteins. Although, there is 20–30% dehydration of the overall ligand upon binding, the hydrogen-bonding sites are dehydrated to a much smaller extent, particularly in cis-like configurations. Conformational preferences of Nuvia cPrime are similar to that of Capto MMC, except for the effect of symmetry arising from the absence of an alkyl thiol tail. Characterizing the conformational equilibria of these two ligands in free solution and bound to a protein provides a foundation for developing a mechanistic understanding of protein–multimodal ligand interactions.
The adsorption, partitioning, and diffusion of CO 2 and CH 4 in organic–inorganic pores composed of kerogen with silica, illite, or calcite are studied using density functional theory and classical molecular dynamics simulations. The adsorption and partitioning behavior of CO 2 and CH 4 molecules is found to be a function of chemistry of the solid interface, pore size, and surface area. CO 2 molecules are preferentially adsorbed compared to CH 4 molecules on silica, illite, calcite, and kerogen surfaces due to significant contributions of electrostatic interactions with the atoms of the associated surfaces. CO 2 and CH 4 molecules display higher adsorption energy on calcite and silica compared to those on illite and kerogen because of enhanced interactions with the positively charged calcium ions on the calcite surface and the hydroxyl group (-OH) on the silica surface. Enhanced internal nanopores and the availability of adsorption active sites in illite and kerogen matrices aid in higher partitioning of the gas molecules into these pores. CO 2 has a significant influence on the clustering and swelling of kerogen fragments compared to CH 4 . Higher CO 2 adsorption on inorganic and kerogen surfaces results in lower overall self-diffusivities compared to CH 4 . This study illustrates surface and pore size controls on the adsorption, partitioning, and self-diffusivities of CO 2 and CH 4 at conditions relevant for subsurface energy applications. The chemistry of the surfaces along with the availability of internal pores and active adsorption sites influences the adsorption behavior of gases. Our results suggest that CO 2 stored in depleted gas reservoirs may preferentially inhabit nanoconfined pores.
For study of time-dependent conformation, all previous single-molecule imaging studies of polymer transport involve fluorescence labeling uniformly along the chain, which suffers from limited resolution due to the diffraction limit. Here we demonstrate the concept of submolecular single-molecule imaging with DNA chains assembled from DNA fragments such that a chain is labeled at designated spots with covalently attached fluorescent dyes and the chain backbone with dyes of different color. High density of dyes ensures good signal-to-noise ratio to localize the designated spots in real time with nanometer precision and prevents significant photobleaching for long-time tracking purposes. To demonstrate usefulness of this approach, we image electrophoretic transport of λ-DNA through agarose gels. The unexpected pattern is observed that one end of each molecule tends to stretch out in the electric field while the other end remains quiescent for some time before it snaps forward and the stretch–recoil cycle repeats. As a result, these features are neither predicted by prevailing theories of electrophoresis mechanism nor detectable by conventional whole-chain labeling methods, which demonstrate pragmatically the usefulness of modular stitching to reveal internal chain dynamics of single molecules.
Infrasonic signatures of meteoroid fragmentation are frequently ambiguous: do multiple arrivals signify a complex breakup or merely the distorting effects of a layered atmosphere? Resolving this ambiguity is critical for accurate energy estimates and source reconstruction. In this study, we address this challenge by analyzing a unique regional dataset of well-constrained meteoroid events observed by the Southern Ontario Meteor Network and the co-located Elginfield Infrasound Array. We employ pseudo-differential parabolic equation (PPE) simulations to quantify how fine-scale gravity-wave structures in the stratosphere and lower thermosphere modify acoustic waveforms at ranges <300 km. Our modeling reveals that while fine-scale layering can stretch signals and generate diffuse oscillatory tails, it does not produce discrete, high-amplitude pulse splitting at ranges below ∼140 km. By applying these results to the rare multi-arrival event 20060305, we demonstrate that its distinct double arrival at 100 km range is inconsistent with atmospheric multipathing and provides definitive evidence of separate fragmentation episodes. These findings establish new diagnostic criteria for separating source physics from propagation artifacts, improving the reliability of infrasound as a monitoring tool for natural bolides, space debris re-entries, and catastrophic launch failures.
A detailed quantum mechanical characterization of the photodissociation dynamics of H{sub 2}O at 121.6 nm is presented. The calculations were performed using a full-dimensional wave packet method on coupled potential energy surfaces of all relevant electronic states. Our state-to-state model permits a detailed analysis of the OH(X{sup ~}/A{sup ~}) product fine-structure populations as a probe of the non-adiabatic dissociation dynamics. The calculated rotational state distributions of the two Λ-doublet levels of OH(X{sup ~}, v = 0) exhibit very different characteristics. The A′ states, produced mostly via the B{sup ~}→X{sup ~} conical intersection pathway, have significantly higher populations than the A″ counterparts, which are primarily from the B{sup ~}→A{sup ~} Renner-Teller pathway. The former features a highly inverted and oscillatory rotational state distribution, while the latter has a smooth distribution with much less rotational excitation. In good agreement with experiment, the calculated total OH(X{sup ~}) rotational state distribution and anisotropy parameters show clear even-odd oscillations, which can be attributed to a quantum mechanical interference between waves emanating from the HOH and HHO conical intersections in the B{sup ~}→X{sup ~} non-adiabatic pathway. On the other hand, the experiment-theory agreement for the OH(A{sup ~}) fragment is also satisfactory, although some small quantitative differences suggest remaining imperfections of the ab initio based potential energy surfaces.
Abstract Cervical spondylotic myelopathy (CSM) is a common cause of disability with few treatments. Aberrant mitochondrial dynamics play a crucial role in the pathogenesis of various neurodegenerative diseases. Thus, regulation of mitochondrial dynamics may offer therapeutic benefit for the treatment of CSM. Muscone, the active ingredient of an odoriferous animal product, exhibits anti‐inflammatory and neuroprotective effects for which the underlying mechanisms remain obscure. We hypothesized that muscone might ameliorate inflammatory responses and neuronal damage by regulating mitochondrial dynamics. To this end, the effects of muscone on a rat model of chronic cervical cord compression, as well as activated BV2 cells and injured neurons, were assessed. The results showed that muscone intervention improved motor function compared with vehicle‐treated rats. Indeed, muscone attenuated pro‐inflammatory cytokine expression, neuronal‐apoptosis indicators in the lesion area, and activation of the nod‐like receptor family pyrin domain‐containing 3 inflammasome, nuclear transcription factor‐κB, and dynamin‐related protein 1 in Iba1‐ and βIII‐tubulin‐labeled cells. Compared with vehicle‐treated rats, compression sites of muscone‐treated animals exhibited elongated mitochondrial morphologies in individual cell types and reduced reactive oxygen species. In vitro results indicated that muscone suppressed microglial activation and neuronal damage by regulating related‐inflammatory or apoptotic molecules. Moreover, muscone inhibited dynamin‐related protein 1 activation in activated BV2 cells and injured neurons, whereby it rescued mitochondrial fragmentation and reactive oxygen species production, which regulate a wide range of inflammatory and apoptotic molecules. Our findings reveal that muscone attenuates neuroinflammation and neuronal damage in rats with chronic cervical cord compression by regulating mitochondrial fission events, suggesting its promise for CSM therapy. image
Monitoring of PV/DER site production is expensive to install and unreliable. Among third party systems providers, lost communications links are a growing concern. Nearly 20% of links are failing, provisioning is complex, recovery is expensive, production data is lost, and access is fragmented. FleetLink is a new concept in DER system communications, purpose built for lowering the cost of maintaining active contact with residential end user sites and ensuring that production data is reliably available to third party systems providers. Systems providers require accurate, secure system monitoring and reporting of production data and system faults while driving down overall costs to compete effectively. This plug and play, independently operating communications solution lowers the cost of fleet contact from typically .08 dollars-$.12/W down to .02 dollars -.03/W including installation and maintenance expenses. FleetLink establishes a breakthrough in simplicity that facilitates rapid expansion of residential solar by reducing initial capital outlay and lowering installation labor time and skill levels. The solution also facilitates higher DER installation growth rates by driving down maintenance costs and eliminating communications trouble calls. This is accomplished by the FleetLink’s unique network technology that enables dynamic network configuration for fast changes, and active, self-healing DER site contact for uptime assurance. Using an open source network framework with proprietary, application specific enhancements, FleetLink independently manages connectivity, security, recovery, grid control communications, and fleet expansion while presenting a compliant SunSpec interface to the third party operations centers. The net system cost savings of at least .05 dollars/W supports the SunShot cost goals and the flexibility and scalability of the solution accelerates the velocity and ubiquitous adoption of solar.
The research addressed with this award seeks to advance our understanding of the structure and dynamics underlying the properties of visible matter. In our current understanding the nucleons (protons and neutrons) are not fundamental but are comprised of quarks and gluons, which are collectively called partons. A static quark picture fails to explain the properties of the nucleons, such as their mass and intrinsic spin, which are thought to emerge dynamically from the quark-gluon interactions via the strong force. In this work, novel observables employing correlations of particles produced in the scattering of high energy electrons off protons at the CLAS12 experiment at Jefferson Lab were analyzed to probe quark-gluon interactions. The ultimate goal of this line of inquiry is to be able to describe the properties of protons and neutrons from first principles, similar to how studying the hydrogen atom has led to the formulation of the theory of Quantum Electrodynamics. Because quarks cannot be observed directly but only as part of more complex composite particles, a smaller, complimentary part of this work was the analysis of particle production in electron-positron annihilation at the Belle II experiment to understand the production of particles from initial quarks. This takes advantage of the fact that in e + e - annihilation the initial quark dynamics is known, unlike in the scattering of nucleons. Several new applications using Machine Learning algorithms for event tagging and reconstruction to support this program were developed as part of this award. In addition, we had a significant role in the development of the physics program for the future Electron-Ion Collider, which is a new collider to be build in the US within the next decade.
Understanding the dynamics of partons in general, and non perturbative sea, in particular, will be crucial for the understanding of strong interactions. Correlations of the spin of the target or/and the momentum and the spin of quarks, combined with final state interactions define the azimuthal distributions of produced particles. Production of correlated hadron pairs, in addition, will play an increasingly important role in the interpretation of pion electroproduction data in general, and hadronization process of quarks, in particular. More significant, than originaly anticipated, fraction of pions coming from correlated di-hadrons, indicated by recent CLAS12 measurements, and supported by various realistic models describing the hadronization process, may have a significant impact on various aspects of data analysis, including the modeling, composition, and interpretation of semi-inclusive DIS data, as well as calculations of radiative corrections. Studies of the nucleon structure beyond the traditional leading twist and current fragmentation of inclusive hadrons, provide qualitatively new tools to study the nucleon structure and extension of large x region well covered by JLab, to large Q2 at the EIC where it will be very important in interpretation of the data from JLab.
The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (~20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (~100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation.
The formation mechanism of brown dwarfs (BDs) is one of the long-standing problems in star formation because the typical Jeans mass in molecular clouds is too large to form these substellar objects. To answer this question, it is crucial to study a BD in the embedded phase. IRAS 16253–2429 is classified as a very low-luminosity object (VeLLO) with an internal luminosity of <0.1 L {sub ⊙}. VeLLOs are believed to be very low-mass protostars or even proto-BDs. We observed the jet/outflow driven by IRAS 16253–2429 in CO (2–1), (6–5), and (7–6) using the IRAM 30 m and Atacama Pathfinder Experiment telescopes and the Submillimeter Array (SMA) in order to study its dynamical features and physical properties. Our SMA map reveals two protostellar jets, indicating the existence of a proto-binary system as implied by the precessing jet detected in H{sub 2} emission. We detect a wiggling pattern in the position–velocity diagrams along the jet axes, which is likely due to the binary orbital motion. Based on this information, we derive the current mass of the binary as ∼0.032 M{sub ⊙}. Given the low envelope mass, IRAS 16253–2429 will form a binary that probably consist of one or two BDs. Furthermore, we found that the outflow force as well as the mass accretion rate are very low based on the multi-transition CO observations, which suggests that the final masses of the binary components are at the stellar/substellar boundary. Since IRAS 16253 is located in an isolated environment, we suggest that BDs can form through fragmentation and collapse, similar to low-mass stars.
We report an investigation of the influence of aqueous solutions of amphiphilic oligomers on the ordering of micrometer-thick films of thermotropic liquid crystals (LCs), thus addressing the gap in knowledge arising from previous studies of the interactions of monomeric and polymeric amphiphiles with LCs. Specifically, we synthesized amphiphilic oligomers (with decyl hydrophobic and pentaethylene glycol hydrophilic domains) in monomer, dimer, and trimer forms, and incubated aqueous solutions of the oligomers against nematic films of 4'-pentyl-4-biphenylcarbonitrile (5CB). All amphiphilic oligomers caused sequential surface-driven orientational (planar to homeotropic) and then bulk phase transitions (nematic to isotropic) with dynamics depending strongly on the degree of oligomerization. The dynamics of the orientational transitions accelerated from monomer to trimer, consistent with the effects of an increase in adsorption free energy. The mechanism underlying the orientational transition, however, involved a decrease in anchoring energy and not change in the easy axis of the LC. In contrast, the rate of the phase transition induced by absorption of oligomers into the LC decreased from monomer to trimer, suggesting that constraints on configurational degrees of freedom influence the absorption free energies of the oligomers. Interestingly, the oligomer-induced transition from the nematic to isotropic phase of 5CB was observed to nucleate at the aqueous-5CB interface, consistent with surface-induced disorder underlying the above-reported decrease in anchoring energy caused by the oligomers. Finally, we provided proof-of-concept experiments of the triggering of LCs using a trimeric amphiphile that is photocleaved by UV illumination into monomeric fragments. Overall, our results provide insight into the rational design of oligomers that can be used as triggers to create responsive LCs.
The 25 amino acids long, transmembrane fragment of the Influenza virus M2 protein forms a homotetrameric channel that transports protons across lipid bilayers. It has been postulated that high efficiency and selectivity of this process is due to gating by four histidine residues that occlude the channel lumen in the closed state. Two mechanisms of gating have been postulated. In one mechanism, the proton is "shuttled" through the gate by attaching to the delta nitrogen atom on the extracellular side of the imidazole ring, followed by the release of the proton attached to the epsilon nitrogen atom on the opposite side. In the second mechanism, the four histidines move away from each other due to electrostatic repulsion upon protonation, thus opening the gate sufficiently that a wire of water molecules can penetrate the gate. Then, protons are transported by "hopping" along the wire. In this paper, both mechanisms are evaluated in a series of molecular dynamics simulations by investigating stability of different protonation states of the channel that are involved in these mechanisms. For the shuttle mechanism, these are states with all epsilon protonated histidines, one biprotonated residue or one histidine protonated in the delta position. For the gate opening mechanism, this is the state in which all four histidines are biprotonated. In addition, a state with two biprotonated histidines is considered. For each system, composed of the protein channel embedded in phospholipid bilayer located between two water lamellae, a molecular dynamics trajectory of approximately 1.3 ns (after equilibration) was obtained. It is found that the states involved in the shuttle mechanism are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfers involved in the shuttle. In contract, the fully biprotonated state, implicated in the gate opening mechanism, is not stable and the channel looses its structural integrity. If only two histidines are biprotonated the channel deforms but remains intact with the gate mostly closed. In summary, the results of this study lend support to the shuttle mechanism but not to the gate opening mechanism of proton gating in M2.
Up to ten years ago, very little was known about the excited states of protonated amino acids isolated in the gas phase. From the experimental point of view, the study was hampered by the lack of ease of production of such species in sufficient density to apply photon-based techniques. With the development and widespread use of electrospray ionization sources coupled with modified or homebuilt mass spectrometers, there has been significant research into the spectroscopy of biomimetic and biologically relevant molecules. Besides, these species are floppy such that an efficient cooling is required to record clear spectroscopy. Warm protonated species display congested spectra. To extract precise spectroscopic information and avoid spectral congestion, the species need to be cooled down to less than 50 K. We present our latest results on the electronic spectroscopy of protonated phenylalanine and tyrosine on a large spectral domain (225-290 nm). These species are studied in a new simplified apparatus combining an electrospray ionization source, a cryogenically cooled quadrupole ion trap (∼10 K) and time-of-flight mass spectrometry. The role of proton transfer from the NH{sub 3}{sup +} moiety to the p-ring or to CO of the carboxylic acid group is evidenced by UV photofragment spectroscopy. This first step controls the fragmentation pathways, which strongly depend on the nature of the electronic excited states, i.e. ππ*, ππ*{sub CO} and πσ{sub NH3}.
Paramecium bursaria chlorella virus 1 (PBCV-1) is the prototype of the genus Chlorovirus (family Phycodnaviridae) that infects the unicellular, eukaryotic green alga Chlorella variabilis NC64A. The 331-kb PBCV-1 genome contains 416 major open reading frames. A mRNA-seq approach was used to analyze PBCV-1 transcriptomes at 6 progressive times during the first hour of infection. The alignment of 17 million reads to the PBCV-1 genome allowed the construction of single-base transcriptome maps. Significant transcription was detected for a subset of 50 viral genes as soon as 7 min after infection. By 20 min post infection (p.i.), transcripts were detected for most PBCV-1 genes and transcript levels continued to increase globally up to 60 min p.i., at which time 41% or the poly (A+)-containing RNAs in the infected cells mapped to the PBCV-1 genome. For some viral genes, the number of transcripts in the latter time points (20 to 60 min p.i.) was much higher than that of the most highly expressed host genes. RNA-seq data revealed putative polyadenylation signal sequences in PBCV-1 genes that were identical to the polyadenylation signal AAUAAA of green algae. Several transcripts have an RNA fragment excised. However, the frequency of excision and the resulting putative shortened protein products suggest that most of these excision events have no functional role but are probably the result of the activity of misled splicesomes.