Statistical equilibrium and ergodic Markov chains.
Time dependent statistical equilibrium equations solutions for describing time development of atomic populations by means of ergodic Markov chain
Dietz, R. D.↗
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Carbon-carbon interactions in warm dense titanium carbide
Encouraged by experimental reports of diamond precipitation in carbon-containing materials under warm dense matter conditions and in shock compression experiments, we examine the behavior of carbon in TiC using density functional theory-molecular dynamics simulations. Two polymorphs of TiC are considered, the ambient-pressure B1 ($Fm$$\overline{3}$$m$) structure in which C-C interactions are prevented by geometric constraints, and a high-pressure Cmcm structure in which C atoms condense into zigzag chains. Chemistry-inspired bonding analyses confirm the covalently bound nature of these chains and further illuminate important interatomic interactions in both structures. Upon melting of B1 TiC, new short-range C-C interactions develop in the liquid, while the pre-existing C-C interactions in Cmcm TiC persist in the liquid. Here, the resulting carbon networks in the melt provide a promising environment for eventual diamond nucleation.
Ab initio molecular dynamics↗
Experimental interstellar organic chemistry: Preliminary findings
In a simulation of interstellar organic chemistry in dense interstellar clouds or on grain surfaces, formaldehyde, water vapor, ammonia and ethane are deposited on a quartz cold finger and ultraviolet-irradiated in high vacuum at 77K. The HCHO photolytic pathway which produces an aldehyde radical and a superthermal hydrogen atom initiates solid phase chain reactions leading to a range of new compounds, including methanol, ethanol, acetaldehyde, acetonitrile, acetone, methyl formate, and possibly formic acid. Higher nitriles are anticipated. Genetic relations among these interstellar organic molecules (e.g., the Cannizzaro and Tischenko reactions) must exist. Some of them, rather than being synthesized from smaller molecules, may be degradation products of larger organic molecules, such as hexamethylene tetramine, which are candidate consitituents of the interstellar grains. The experiments reported here may also be relevant to cometary chemistry.
Khare, B. N.↗
Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR
Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic–inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. Here, to understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31–calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ∼2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31–calcite interactions. While this work provides the first experimental confirmation that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31–calcite interface has advanced our fundamental understanding of the atomic interactions at the organic–inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.
Close, Emily G. S. [Pacific Northwest National Lab↗
DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR
Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.
Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗
Lower bounds on entanglement entropy without twin copy
We discuss the possibility of estimating experimentally the von Neumann entanglement entropy S A v N of a symmetric bipartite quantum system A B by using the basic measurement counts (bitstrings) for a single copy of a prepared state. Using exact diagonalization and analog simulations performed with the publicly available QuEra facilities for chains and ladders of Rydberg atoms, we calculate the Shannon entropy S A B X associated with the bitstrings of adiabatically prepared ground states and the reduced entropies S A X and S B X obtained from the marginal probabilities in A and B . We then calculate the classical mutual information I A B X = S A X + S B X − S A B X , which is a lower bound on S A v N . We show that for a broad range of lattice spacing and detuning, I A B X is typically 20% below S A v N in regions where S A v N is large and a less close bound in regions where S A v N is low. We argue that this use of the easily available bitstrings provides a robust and efficient way to explore empirically the phase diagram of qubit-based quantum simulators and identify critical regions. Published by the American Physical Society 2025
Meurice, Yannick (ORCID:0000000209959694)↗
Polymers with complexing properties. Simple poly(amino acids)
The free amino (0.3 equiv/residue) and carboxyl (0.5 equiv/residue) groups of thermal polylysine increased dramatically on treatment with distilled water. The total hydrolysis of such a polymer was abnormal in that only about 50% of the expected amino acids were recovered. Poly (lysine-co-alanine-co-glycine) under usual conditions hydrolyzed completely in 8 hours; whereas, when it was pretreated with diazomethane, a normal period of 24 hours was required to give (nearly) the same amounts of each free amino acid as compared with those obtained from the untreated polymer. The amino groups of the basic thermal poly(amino acids) were sterically hindered. The existence of nitrogen atoms linking two or three chains and reactive groups (anhydride, imine) were proposed.
Roque, J. M.↗
Probing the presently tenuous link between comets and the origin of life
The possibilities of using millimeter-wave technology to probe the subsurface processes of comets to investigate links between cometary materials and the origins of life are explored. It is noted that current theories hold that the necessities for life to begin comprise a fairly uniform temperature, the presence of a solvent to give materials mobility, and the presence of atoms which can form long chains of molecules. Consideration is given to two cometary nuclei models: a core with an equal amount of liquid water and lunar material, and a nucleus with equal amounts of frozen water ice and lunar material. Solutions to the radiative transfer equation for the two models are presented to characterize identifiable emissions using radiometric spectrometer instrumentation on a spacecraft. Particular species such as OH, CN, HCN, and glycine are expected to be detectable if present.
Hobbs, R. W.↗
What is the Best Alternative to Diagonalization of the Hamiltonian in Large Scale Semiempirical Calculations?
Recently, several linear scaling approaches have been introduced which replace the time dominating diagonalization step in semiempirical methods, enabling practical calculations to be performed, on very large molecules. This paper compares the accuracy and performance of pseudodiagonalization (PD), conjugate gradient density matrix search (CG-DMS), the Chebyshev polynomial expansion method (CEM), and purification of the density matrix (PDM) as linear scaling substitutions for diagonalization. The scaling, speed, and reliability of these methods are compared for AMI single point energy calculations on polyglycine chains (up to 20,000 atoms), water clusters (up to 12,300 atoms), and nucleic acids (up to 6300 atoms).
Daniels, Andrew D.↗
Side-Chain and Ring-Size Effects on Permeability in Artificial Water Channels
Artificial water channels (AWCs) have emerged as a promising framework for stable water permeation, with water transport rates comparable to aquaporins (3.4–40.3 × 10 8 H 2 O/channel/s). In this study, we probe the influence of ring-size and side-chain length on the water permeability observed within a class of AWCs termed ligand-appended pillar[n]arenes (LAPs) that have an adjustable ring-size (m) and side-chain length (n). Through all-atom molecular dynamics simulations, we calculate the permeability of these channels using the collective diffusion model and find their permeabilities. We characterize the mechanistic influence of pillar[n]arene ring-size and side-chain length on the channel water permeability by analyzing the characteristics of the internal permeating water-wire and the surrounding channel structure. We observe that water permeability decreases as a function of increasing ring-size due to increases in hydrophilic contacts between the permeating water-wire and the oxygen groups on the channel wall. Further, we observe an increase in water permeability as a function of side-chain length due to increased partitioning of the channel terminal groups into the hydrophilic blocks of the surrounding bilayer. For the LAP6 channel, with increase in side-chain length, the distance between terminal groups increases and leads to an increase in pore size, thereby enhancing water permeability. In the case of LAP5, as side-chain length increases, the channel displays a compensatory effect between tilt and bend angle due to the flexible side-chains. Such flexibility leads to higher terminal group partitioning in the hydrophilic blocks of the bilayer and extends the permeating water-wire. Furthermore, this increase in water-wire length and hydrophilic block access overcomes the nonmonotonic pore size trend in pillar[5]arene channels.
36 MATERIALS SCIENCE↗
Vacuum-ultraviolet photochemistry. IX - Primary and chain processes in the photolysis of hydrogen peroxide
Atomic and molecular hydrogen formation in photolysis of hydrogen peroxide
HYDROGEN PEROXIDE↗
Observation of Individual Fluorine Atom from Highly Oriented Poly (tetrafluoroethylene) Films by Atomic Force Microscopy
Direct observation of the film thickness, molecular structure and individual fluorine atoms from highly oriented poly(tetrafluoroethylene) (PTFE) films were achieved using atomic force microscopy (AFM). A thin PTFE film is mechanically deposited onto a smooth glass substrate at specific temperatures by a friction transfer technique. Atomic resolution images of these films show that the chain-like helical structures of the PTFE macromolecules are aligned parallel to each other with an intermolecular spacing of 5.72 A, and individual fluorine atoms are clearly observed along these twisted molecular chains with an interatomic spacing of 2.75 A. Furthermore, the first direct AFM measurements for the radius of the fluorine-helix, and of the carbon-helix in sub-angstrom scale are reported as 1.70 A and 0.54 A respectively.
Lee, Jonathan A.,↗
Observation of Individual Fluorine Atoms from Highly Oriented Poly(Tetrafluoroethylene) Films by Atomic Force Microscopy
Direct observation of the film thickness, molecular structure, and individual fluorine atoms from highly oriented poly(tetrafluoroethylene) (PTFE) films were achieved using atomic force microscopy (AFM). A thin PTFE film is mechanically deposited onto a smooth glass substrate at specific temperatures by a friction-transfer technique. Atomic resolution images of these films show that the chain-like helical structures of the PTFE macromolecules are aligned parallel to each other with an intermolecular spacing of 5.72 A, and individual fluorine atoms are clearly observed along these twisted molecular chains with an interatomic spacing of 2.75 A. Furthermore, the first direct AFM measurements for the radius of the fluorine-helix, and of the carbon-helix in sub-angstrom scale are reported as 1.7 and 0.54 A respectively.
Lee, J. A.↗
In Situ Atomic Tracking on the Interfacial Etching and Reconfiguration of Cu-ReSe 2 Contact during Thermal Annealing
The Schottky barrier height can be greatly affected by the metal diffusion, reaction, and covalent bonding formation at the contact. Exploring novel methods and revealing the fundamental mechanisms for contact engineering are of vital importance for microelectronic devices. Here, in this study, the annealing induced interfacial reactions at Cu-ReSe 2 contact are dynamically revealed from the atomic scale. Accompanied by the diffusion of Se to Cu, ReSe 2 is gradually decomposed to a thin Re interlayer through a “chain-by-chain” manner. Theoretical calculations show that the Cu atoms can facilitate the chemical bond breaking of ReSe 2 , significantly lowering the Se diffusion energy barrier toward Cu. The formed Re/ReSe 2 heterostructure presents a metal-like band structure, which underscores the critical role of Cu in altering the interfacial chemistry and promoting carrier transport across the interface. Our results can provide vital insights into the contact properties of ReSe 2 and provide a possible method for fabricating high-performance ReSe 2 -based devices.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Metallization with generic metallo-organic inks
The use and fabrication of metallo-organic films are discussed. Metallo-organic compounds are ones in which a metal is linked to a long chain carbon ligand through a hetero atom such as O, S, N, P or As. Films formed by the thermal decomposition of these metallo-organics are called MOD films. In order that the products of decomposition contain only CO2, H2O, and in rare cases nitrogen compounds, and to avoid S containing products, the use of a set of metallo-organic compounds for ink fabrication where the linking hetero atom was oxygen was pioneered. These links were made from commercially available carboxylates, or synthesized from commonly available reagents. The processing is described and the molecular design criteria are given. The particular carboxylates or amine carboxylates selected were the octoates or neodecanoates, and they are described.
Vest, G. M.↗
Tholins as Coloring Agents on Solar System Bodies
Pre-biotic organic materials appear to be common on many small bodies in the outer Solar System, as evidenced by the color properties of these objects. We report on our continuing study of color properties in connection with the presence of complex organic solids (tholins) among the planets and their satellites, the asteroids, and the trans- Neptunian objects (Kuiper Belt objects). Most small, icy bodies in the Solar System, whether they have high or low surface reflectance (albedo), show a pronounced downward slope in reflectance at wavelengths shorter than approx. 1 micron. This increasing absorption of sunlight toward shorter wavelengths is characteristic of pi-bonds in hydrocarbons having chains or rings of conjugated C atoms. Tholins, which contain polycyclic aromatic and aliphatic hydrocarbons, exhibit these color properties. Using the complex refractive indices of tholins in models of the reflectance spectra of icy bodies in the Solar System, we find that these complex organic materials satisfactorily account for the coloration so widely observed. The new results presented here show that the wide variety of colors of Kuiper Belt objects can be fit very well with tholins, as can the colors of Pluto and Triton. The implications of these fits of Kuiper Belt objects is that complex organic material is created on their surfaces by energetic particle bombardment of native ices, and also may be accreted from external sources. In the cases of Pluto and Triton, photochemistry of their weak N2 + CH4 + CO atmospheres produces complex organic molecules that precipitate to the surface, providing local color.
Cruikshank, D. P.↗
Working Fluids for Increasing Capacities of Heat Pipes
A theoretical and experimental investigation has shown that the capacities of heat pipes can be increased through suitable reformulation of their working fluids. The surface tensions of all of the working fluids heretofore used in heat pipes decrease with temperature. As explained in more detail below, the limits on the performance of a heat pipe are associated with the decrease in the surface tension of the working fluid with temperature, and so one can enhance performance by reformulating the working fluid so that its surface tension increases with temperature. This improvement is applicable to almost any kind of heat pipe in almost any environment. The heat-transfer capacity of a heat pipe in its normal operating-temperature range is subject to a capillary limit and a boiling limit. Both of these limits are associated with the temperature dependence of surface tension of the working fluid. In the case of a traditional working fluid, the decrease in surface tension with temperature causes a body of the liquid phase of the working fluid to move toward a region of lower temperature, thus preventing the desired spreading of the liquid in the heated portion of the heat pipe. As a result, the available capillary-pressure pumping head decreases as the temperature of the evaporator end of the heat pipe increases, and operation becomes unstable. Water has widely been used as a working fluid in heat pipes. Because the surface tension of water decreases with increasing temperature, the heat loads and other aspects of performance of heat pipes that contain water are limited. Dilute aqueous solutions of long-chain alcohols have shown promise as substitutes for water that can offer improved performance, because these solutions exhibit unusual surface-tension characteristics: Experiments have shown that in the cases of an aqueous solution of an alcohol, the molecules of which contain chains of more than four carbon atoms, the surface tension increases with temperature when the temperature exceeds a certain value. There are also other liquids that have surface tensions that increase with temperature and could be used as working fluids in heat pipes. For example, as a substitute for ammonia, which is the working fluid in some heat pipes, one could use a solution of ammonia and an ionic surfactant.
Chao, David F.↗
Discovery and Synthesis of a Family of Boride Altermagnets
Borides are a rich material family. To push the boundaries of borides’ properties and applications into broader fields, we have conducted systematic theoretical and experimental searches for synthesizable phases in ternary borides TM 2 B 2 (T = 3d, M = 4d/5d transition metals). We find that TM 2 B 2 in the FeMo 2 B 2 -type and CoW 2 B 2 -type structures form a large family of stable/metastable materials of 120 members. Among them, we identify 40 materials with stable magnetic solutions. Further, we discover 11 altermagnets in the FeMo 2 B 2 -type structure. So far, boride altermagnets are rare. In these altermagnets, T = Fe or Mn atoms are arranged in parallel T-chains with strong ferromagnetic intrachain couplings and antiferromagnetic interchain couplings. They simultaneously exhibit electronic band spin splitting, typical of ferromagnetism, and zero net magnetization, typical of antiferromagnetism. They also exhibit magnonic band chiral splitting. Both effects originate from the unique altermagnetic symmetries crucially constrained by the nonmagnetic atoms in the structure. Transport properties of relevance to spintronic applications, including the strain-induced spin-splitter effect and anomalous Hall effect, are predicted. An iodine-assisted synthesis method for TM 2 B 2 is developed, using which 7 of the predicted low-energy phases are experimentally synthesized and characterized, including 4 altermagnets. This work expands the realm of borides by offering new opportunities for studying altermagnetism and altermagnons in borides. It also provides valuable insights into the discovery and design of altermagnets. Here, by demonstrating that altermagnets can exist as families sharing a common motif, this work paves a feasible route for discovering altermagnets by elemental substitutions and high-throughput computations.
Chemical structure↗