jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Tristan Siokos
Source: Preprints.org (preprint, 2024-09-25)
Field: Chemistry — Spectroscopy

Magnetic Ion Modulation (MIM) Theory: A Novel Approach to Controlling Ion Behavior via Magnetic Fields in Biological and Non-Biological Systems e Magnetic Ion Modulation (MIM) Theory presents a unified and groundbreaking mathematical framework for controlling and predicting ion behavior in both biological and non-biological systems using external magnetic fields. Central to the theory is the **Ion Modulation Constant** (Tn), a context-specific scaling factor that quantifies the number of ions modulated under specific conditions. This constant, although not universal, allows for accurate modeling of ion modulation in systems ranging from neuronal ion channels to plasma physics and quantum computing. The MIM equation incorporates ion properties such as magnetic moment and permeability, providing insights into neuromodulation for treating chronic pain and epilepsy, plasma confinement in fusion research, and stabilization of ion qubits in quantum computing. This paper includes detailed derivations of the Ion Modulation Constant, examples of its application to specific ions, and a comprehensive exploration of potential experimental validations. Ion ; Modulation (music) ; Magnetic field ; Ion channel ; Nanotechnology ; Biological system ; Materials science ; Physics ; Chemistry ; Biology ; Acoustics ; Quantum mechanics ; Biochemistry ; Receptor Mass Spectrometry Techniques and Applications ; Magnetic and Electromagnetic Effects ; Fractal and DNA sequence analysis
Authors: Alexander Humeniuk | William J. Glover
Source: ChemRxiv (preprint, 2024-01-02)
Field: Chemistry — Physical and Theoretical Chemistry

Multistate, polarizable QM/MM embedding scheme based on the direct reaction field method: Solvatochromic shifts, analytical gradients and optimization of conical intersections in solution We recently introduced a polarizable embedding scheme based on an integral-exact reformulation of the direct reaction field method (IEDRF) that accounts for differential solvation of ground and excited states in QM/MM simulations. The polarization and dispersion interactions between the quantum-mechanical (QM) and molecular-mechanical (MM) regions are described by the DRF Hamiltonian, while the Pauli repulsion between explicitly treated QM electrons and the implicit electron density around MM atoms is modeled with effective core potentials. A single Hamiltonian is used for all electronic states, so that Born-Oppenheimer states belonging to the same geometry are orthogonal and state crossings are well-defined. In this work, we describe the implementation of the method using graphical processing unit acceleration in TeraChem, where it is combined with multiple electronic structure methods, including Hartree-Fock, Time-dependent Density Functional Theory, and Complete Active Space Self-Consistent Field. In contrast with older implementations of the DRF method, integrals of the polarization operators are evaluated exactly. Expressions for ingredients needed to construct analytical gradients and non-adiabatic coupling vectors are derived and tested by optimizing a conical intersection between two excited states in the presence of a polarizable solvent shell. The method is applied to estimating the solvent shifts of absorption energies of a series of donor-acceptor dyes having low-lying charge-transfer states. Even for a non-polar solvent such as n-hexane, the inclusion of its static polarizability leads to non-negligible shifts that improve the agreement to essentially quantitative levels (0.03 eV) with full-system calculations. Good agreement with the positions of experimental absorption maxima measured in solution is also observed. Conical intersection ; Hamiltonian (control theory) ; Polarizability ; QM/MM ; Chemistry ; Excited state ; Density functional theory ; Implicit solvation ; Solvation ; Solvent models ; Configuration interaction ; Ground state ; Molecular physics ; Quantum mechanics ; Atomic physics ; Physics ; Computational chemistry ; Molecular dynamics ; Molecule ; Mathematics Photochemistry and Electron Transfer Studies ; Spectroscopy and Quantum Chemical Studies ; Free Radicals and Antioxidants
Authors: Tristan Siokos
Source:  (preprint, 2024-09-24)
Field: Chemistry — Spectroscopy

Magnetic Ion Modulation (MIM) Theory: A Novel Approach to Controlling Ion Behavior via Magnetic Fields in Biological and Non-Biological Systems The Magnetic Ion Modulation (MIM) Theory presents a unified and groundbreaking mathematical framework for controlling and predicting ion behavior in both biological and non-biological systems using external magnetic fields. Central to the theory is the **Ion Modulation Constant** (Tn), a contextspecific scaling factor that quantifies the number of ions modulated under specific conditions. This constant, although not universal, allows for accurate modeling of ion modulation in systems ranging from neuronal ion channels to plasma physics and quantum computing. The MIM equation incorporates ion properties such as magnetic moment and permeability, providing insights into neuromodulation for treating chronic pain and epilepsy, plasma confinement in fusion research, and stabilization of ion qubits in quantum computing. This paper includes detailed derivations of the Ion Modulation Constant, examples of its application to specific ions, and a comprehensive exploration of potential experimental validations. Ion ; Modulation (music) ; Ion channel ; Nanotechnology ; Materials science ; Physics ; Computer science ; Chemistry ; Acoustics ; Quantum mechanics ; Biochemistry ; Receptor Mass Spectrometry Techniques and Applications ; Magnetic and Electromagnetic Effects ; Fractal and DNA sequence analysis
Authors: Faisal Kengo | S Solihin | M. Shoufie Ukhtary | Joko Suwardy | Muhammad Aziz Majidi | Ahmad R. T. Nugraha
Source: Physica Scripta (article, 2024-01-29)
Field: Materials Science — Materials Chemistry

Tunable optical absorption in undoped graphene sandwiched between multilayer dielectric stacks with mirror symmetry Abstract We theoretically investigate the optical absorption of an undoped graphene monolayer when put in a one-dimensional multilayer stack. Using the transfer matrix method, we perform numerical simulations and derive explicit analytical formulas for the optical absorption of the graphene monolayer at the center of the dielectric stack and find that the optical absorption uniquely depends on repetition number ( r ) and the unit layers structure. When sandwiched between unit layers structure composed of three dielectric materials (referred to as the ‘ABC’ structure) with even values of r , the graphene monolayer absorbs 2.3% of visible to near-infrared light. This behavior is the same as if graphene were free-standing, not sandwiched between the dielectric stack. In contrast to that situation, in the ABC structure with odd values of r , also when the graphene monolayer is sandwiched between four materials (the ‘ABCD’ structure) with any values of r , we can obtain optical absorption as large as 50% at particular refractive indices ( n ) of the constituent dielectric materials. The 50% absorption is, in fact, the maximum optical absorption for any undoped monolayer material in the symmetric dielectric stacks. By varying r and n within the ABC or ABCD structures, we can finely adjust the optical absorption of graphene within the range of 0%–50%, facilitating precise control for various optoelectronic applications. Materials science ; Dielectric ; Graphene ; Absorption (acoustics) ; Optoelectronics ; Symmetry (geometry) ; Mirror symmetry ; Optics ; Nanotechnology ; Physics ; Quantum mechanics Graphene research and applications ; Plasmonic and Surface Plasmon Research ; Photonic Crystals and Applications
Authors: Tristan Siokos
Source: Preprints.org (preprint, 2024-09-24)
Field: Chemistry — Spectroscopy

Magnetic Ion Modulation (MIM) Theory: A Novel Approach to Controlling Ion Behavior via Magnetic Fields in Biological and Non-Biological Systems The Magnetic Ion Modulation (MIM) Theory presents a unified and groundbreaking mathematical framework for controlling and predicting ion behavior in both biological and non-biological systems using external magnetic fields. Central to the theory is the **Ion Modulation Constant** (Tn), a context-specific scaling factor that quantifies the number of ions modulated under specific conditions. This constant, although not universal, allows for accurate modeling of ion modulation in systems ranging from neuronal ion channels to plasma physics and quantum computing. The MIM equation incorporates ion properties such as magnetic moment and permeability, providing insights into neuromodulation for treating chronic pain and epilepsy, plasma confinement in fusion research, and stabilization of ion qubits in quantum computing. This paper includes detailed derivations of the Ion Modulation Constant, examples of its application to specific ions, and a comprehensive exploration of potential experimental validations. Ion ; Modulation (music) ; Ion channel ; Physics ; Chemistry ; Quantum mechanics ; Acoustics ; Biochemistry ; Receptor Mass Spectrometry Techniques and Applications ; Magnetic and Electromagnetic Effects ; Fractal and DNA sequence analysis
Authors: Abdelhak Ferroudj | Y. Djaballah
Source: physica status solidi (b) (article, 2024-06-16)
Field: Materials Science — Materials Chemistry

Investigation on New Orthorhombic AuR (R = Ho, Tb, Y) and PdR (R = Eu,Gd,Y) Equiatomic Compounds’ Structural, Vibrational, and Thermal Properties Herein, first‐principles calculations using the planewave pseudopotential technique to assess the structural, elastic, vibrational, and thermal properties of equiatomic intermetallic consisting of rare earth elements (Eu, Gd, Ho, Y, Tb) and noble metals (Au, Pd) are used. This approach involves optimizing novel orthorhombic structures by minimizing the total energy and interatomic forces. The computed structural features for the investigated intermetallics closely align with available experimental data. By evaluating stability criteria using the derived elastic constants, this analysis verifies the stability of these intermetallics in an orthorhombic structure at zero pressure. Furthermore, various mechanical parameters are determined, including (Young's E , bulk B , shear G , Pugh's) modulus, Poisson's ratio, and anisotropy factors. These parameters are derived from the computed single‐crystal elastic constants using the Voigt–Reuss–Hill average method. This investigation delves into the relationship between temperature and variations in heat capacity at constant volume ( C v ) and entropy (S), comprehensively exploring these variables. Intermetallic ; Pseudopotential ; Orthorhombic crystal system ; Materials science ; Heat capacity ; Thermodynamics ; Bulk modulus ; Shear modulus ; Anisotropy ; Crystallography ; Crystal structure ; Condensed matter physics ; Chemistry ; Metallurgy ; Alloy ; Composite material ; Physics Boron and Carbon Nanomaterials Research ; Intermetallics and Advanced Alloy Properties ; X-ray Diffraction in Crystallography
Authors: Alex Shaji | Kevin J. Rietwyk | Islay O. Robertson | Philipp Reineck | David A. Broadway | Jean‐Philippe Tetienne
Source: arXiv (Cornell University) (preprint, 2024-05-03)
Field: Materials Science — Materials Chemistry

A compact, portable device for microscopic magnetic imaging based on diamond quantum sensors Magnetic imaging based on ensembles of diamond nitrogen-vacancy quantum sensors has emerged as a useful technique for the spatial characterisation of magnetic materials and current distributions. However, demonstrations have so far been restricted to laboratory-based experiments using relatively bulky apparatus and requiring manual handling of the diamond sensing element, hampering broader adoption of the technique. Here we present a simple, compact device that can be deployed outside a laboratory environment and enables robust, simplified operation. It relies on a specially designed sensor head that directly integrates the diamond sensor while incorporating a microwave antenna and all necessary optical components. This integrated sensor head is complemented by a small control unit and a laptop computer that displays the resulting magnetic image. We test the device by imaging a magnetic sample, demonstrating a spatial resolution of 4 $μ$m over a field of view exceeding 1 mm, and a best sensitivity of 45 $μ$T/$\sqrt{\rm Hz}$ per ($5\,μ$m)$^2$ pixel. Our portable magnetic imaging instrument may find use in situations where taking the sample to be measured to a specialist lab is impractical or undesirable. Diamond ; Quantum sensor ; Quantum ; Optoelectronics ; Materials science ; Physics ; Nanotechnology ; Quantum computer ; Quantum mechanics ; Quantum simulator ; Composite material Diamond and Carbon-based Materials Research ; Force Microscopy Techniques and Applications
Authors: Jamin Kidd | Ruiqi Zhang | Shao-Kai Jian | Jianwei Sun
Source: arXiv (Cornell University) (preprint, 2024-02-06)
Field: Materials Science — Materials Chemistry

First-principles phase diagram of an interacting ionic chain The widely-used Kohn-Sham implementation of density functional theory (DFT) maps a system of interacting electrons onto an auxiliary non-interacting one and is presumably inaccurate for strongly correlated materials. We present a concrete benchmark for DFT by examining the electronic ground state phase diagram of a strongly interacting chain with uneven, non-integer nuclear charges. The interplay between charge imbalance and Coulomb repulsion yields two competing phases, a band insulator and a Mott insulator. By including infinitesimal lattice distortions, DFT stabilizes the intermediate spontaneously dimerized insulator phase that results from this competition. We assess the phase diagram by mapping the bond length and nuclear charge ratio of the chain to the ionic Hubbard model and performing highly accurate density matrix renormalization group calculations. Our comparative study provides foundational insight into the utility of symmetry-broken DFT as a predictive tool for elucidating phase diagrams with competing orders. Phase diagram ; Chain (unit) ; Ionic bonding ; Phase (matter) ; Physics ; Ion ; Quantum mechanics Machine Learning in Materials Science
Authors: Ryan S. Wang | Siang-Wun Siao | Jessica C. Wang | Patrick Y. Lin | Claire R. Shen
Source: Metabolic Engineering Communications (article, 2024-08-05)
Field: Materials Science — Materials Chemistry

Engineering thioesterase as a driving force for novel itaconate production via its degradation scheme Incorporation of irreversible steps in pathway design enhances the overall thermodynamic favorability and often leads to better bioconversion yield given functional enzymes. Using this concept, here we constructed the first non-natural itaconate biosynthesis pathway driven by thioester hydrolysis. Itaconate is a commercially valuable platform chemical with wide applications in the synthetic polymer industry. Production of itaconate has long relied on the decarboxylation of TCA cycle intermediate cis-aconitate as the only biosynthetic route. Inspired by nature's design of itaconate detoxification, here we engineered a novel itaconate producing pathway orthogonal to native metabolism with no requirement of auxotrophic knock-out. The reversed degradation pathway initiates with pyruvate and acetyl-CoA condensation forming (S)-citramalyl-CoA, followed by its dehydration and isomerization into itaconyl-CoA then hydrolysis into itaconate. Phenylacetyl-CoA thioesterase (PaaI) from <i>Escherichia</i> <i>coli</i> was identified via screening to deliver the highest itaconate formation efficiency when coupled to the reversible activity of citramalate lyase and itaconyl-CoA hydratase. The preference of PaaI towards itaconyl-CoA hydrolysis over acetyl-CoA and (S)-citramalyl-CoA also minimized the inevitable precursor loss due to enzyme promiscuity. With acetate recycling, acetyl-CoA conservation, and condition optimization, we achieved a final itaconate titer of 1 g/L using the thioesterase driven pathway, which is a significant improvement compared to the original degradation pathway based on CoA transferase. This study illustrates the significance of thermodynamic favorability as a design principle in pathway engineering. Degradation (telecommunications) ; Scheme (mathematics) ; Chemistry ; Production (economics) ; Thioesterase ; Computer science ; Biophysics ; Biochemistry ; Enzyme ; Biology ; Mathematics ; Biosynthesis Enzyme Structure and Function ; Enzyme Production and Characterization ; Microbial Metabolic Engineering and Bioproduction
Authors: Amir Ayati | Hugh G. A. Burton | Stijn De Baerdemacker
Source: arXiv (Cornell University) (preprint, 2024-12-21)
Field: Chemistry — Spectroscopy

Spin-Symmetry Projected constrained Unrestricted Hartree-Fock We introduce an electronic structure approach for spin symmetry breaking and restoration from the mean-field level. The spin-projected constrained-unrestricted Hartree-Fock (SPcUHF) method restores the broken spin symmetry inherent in spin-constrained-UHF determinants by employing a non-orthogonal Configuration Interaction (NOCI) projection method. This method includes all possible configurations in spin space compatible with a Clebsch-Gordon recoupling scheme in a NOCI calculation. The tunable one-pair-at-a-time characteristics of the symmetry-breaking process in c-UHF allow us to reduce the computational costs of full projection. SPcUHF is tested on 4-, 6-, and 8-electron systems that exhibit dominant static and/or dynamic correlations. Hartree–Fock method ; Symmetry (geometry) ; Physics ; Spin (aerodynamics) ; Quantum mechanics ; Theoretical physics ; Mathematics ; Geometry Advanced NMR Techniques and Applications ; Nuclear physics research studies ; Quantum Mechanics and Non-Hermitian Physics
Authors: Katja Klinar | Andrej Kitanovski
Source: Journal of Physics Conference Series (article, 2024-05-01)
Field: Materials Science — Materials Chemistry

Thermal control devices and thermal circuits Abstract It is becoming evident that conventional thermal management methods like conventional thermal insulation and conventional thermal storage cannot meet the thermal control requirements of advanced, especially small systems with higher power densities or potentially transient, fluctuating, or migrating hot or cold spots, and for temperature-sensitive devices. This challenge is most evident in electronic components that experience degradation and loss of efficiency without constant and effective heat dissipation. To overcome these limitations, thermal control devices have emerged in various areas of thermal management. These small-scale devices provide non-linear, switchable, and active control of heat, similar to the way their electrical counterparts regulate electric current. Among others, notable thermal control devices include thermal conduits (which act as solid-state heat routers), thermal resistors (which provide thermal insulation), thermal switches (which actively control heat transfer through on-off states), and thermal diodes (which rectify heat currents). In this paper, we provide state of the art on the research activities and applications of thermal control devices. Thermal ; Electronic circuit ; Materials science ; Electrical engineering ; Engineering ; Physics ; Thermodynamics Thermal properties of materials ; Heat Transfer and Optimization ; Thermal Radiation and Cooling Technologies
Authors: Lubova Denisova | Antons Pacejs | Emil Yankov | Lyubomir Lazov
Source: Environment Technology Resources Proceedings of the International Scientific and Practical Conference (article, 2024-06-22)
Field: Materials Science — Surfaces, Coatings and Films

INVESTIGATION OF LASER TEXTURING ON THE SURFACE OF ANODIZED ALUMINIUM This study examines the texturing of anodized aluminium using a Rofin PowerLine F 20 Varia nanosecond Yb doped fiber laser. It explores how varying laser parameters like scanning speed, hatching step, laser power, and frequency impact the surface's wetting properties, particularly the contact angle with a water droplet. The research aims to understand the influence of these parameters on the aluminium’s surface, offering insights into the laser micromachining process and its industrial and material science applications. This study examines the texturing of anodized aluminium using a Rofin PowerLine F 20 Varia nanosecond Yb doped fiber laser. It explores how varying laser parameters like scanning speed, hatching step, laser power, and frequency impact the surface's wetting properties, particularly the contact angle with a water droplet. The research aims to understand the influence of these parameters on the aluminium’s surface, offering insights into the laser micromachining process and its industrial and material science applications. This study investigates the texturing of anodized aluminium using a Rofin PowerLine F20 Varia nanosecond fiber laser. It investigates how different laser parameters such as scan speed, hatching step, laser power and frequency affect the surface wetting properties, especially the contact angle of a water droplet. The research aims to understand the influence of these parameters on the aluminium surface, offering insights into the laser micromachining process and its applications in industry and materials science. Anodizing ; Aluminium ; Materials science ; Metallurgy ; Laser ; Optics Surface Modification and Superhydrophobicity ; Adhesion, Friction, and Surface Interactions ; Additive Manufacturing and 3D Printing Technologies
Authors: Evgenii Barts | Karma Tenzin | Jagoda Sławińska
Source: arXiv (Cornell University) (preprint, 2024-07-01)
Field: Chemistry — Spectroscopy

Efficient spin accumulation carried by slow relaxons in chiral tellurium Efficient conversion between charge currents and spin signals is crucial for realizing magnet-free spintronic devices. However, the strong spin-orbit coupling that enables such a conversion, causes rapid relaxation of spins, making them difficult to transport over large length scales. Here, we show that spin-momentum entanglement at the Fermi surface of chiral tellurium crystals leads to the appearance of slow collective relaxation modes. These modes, called relaxons, resemble the persistent spin helix, a collective spin-wave excitation with extended lifetime observed in quantum wells. The slow relaxons dominate the electrically generated spin and orbital angular momentum accumulation in tellurium and make it possible to combine a very high 50% conversion efficiency with a long spin lifetime. These results, obtained from the exact solution of the Boltzmann transport equation, show that chiral crystals can be used for highly efficient generation and transmission of spin signals over long distances in spintronic devices. Tellurium ; Spin (aerodynamics) ; Physics ; Condensed matter physics ; Materials science ; Metallurgy ; Thermodynamics Advanced NMR Techniques and Applications ; Atomic and Subatomic Physics Research ; Molecular spectroscopy and chirality
Authors: D. Yu. Voronina | A. S. Krylov | V. V. Tolstyakov | A. V. Dogadina
Source: Russian Journal of General Chemistry (article, 2024-01-01)
Field: Chemistry — Organic Chemistry

Phosphorylation of 5-Amino-1H-1,2,4-triazoles with Diethyl Phosphorochloridate New phosphorylated 5-amino-1H-1,2,4-triazoles were obtained by the chemoselective reaction of diethyl phosphorochloridate with 5-amino-1H-1,2,4-triazoles. The structure of the synthesized compounds was characterized by 1H, 13C, and 31P NMR spectroscopy and mass spectrometry. Chemistry ; Mass spectrometry ; Amino acid ; Phosphorylation ; Nuclear magnetic resonance spectroscopy ; Organic chemistry ; Biochemistry ; Chromatography Synthesis and Characterization of Heterocyclic Compounds ; Synthesis and biological activity ; Click Chemistry and Applications