jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Afshin Nabiyan | Aswathy N. Muttathukattil | Federico Tomazic | David Pretzel | Ulrich S. Schubert | Michael Engel | Felix H. Schacher
Source: arXiv (Cornell University) (preprint, 2023-06-16)
Field: Materials Science — Materials Chemistry

Self-Assembly of Core-Shell Hybrid Nanoparticles by Directional Crystallization of Grafted Polymers Nanoparticle self-assembly is an efficient bottom-up strategy for the creation of nanostructures. In the standard approach, ligands are grafted on the surfaces of nanoparticles to keep them separated and control interparticle interactions. Ligands then remain secondary and usually are not expected to order significantly during superstructure formation. Here, we investigate how ligands can play a more primary role in the formation of inorganic-organic hybrid materials. We graft poly(2-iso-propyl-2-oxazoline) (PiPrOx) as a crystallizable shell onto SiO$_2$ nanoparticles. By varying the PiPrOx grafting density, solution stability, and nanoparticle aggregation behavior can be controlled. Upon prolonged heating, anisotropic nanostructures form in conjunction with the crystallization of the ligands. Self-assembly of hybrid PiPrOx@SiO$_2$ (shell@core) nanoparticles proceeds in two steps: First, rapid formation of amorphous aggregates via gelation, mediated by the interaction between nanoparticles through grafted polymers; second, slow radial growth of fibers via directional crystallization, governed by the incorporation of crystalline ribbons formed from unbound polymers coupling to the grafted polymer shell. Our work reveals how crystallization-driven self-assembly of ligands can create intricate hybrid nanostructures. Crystallization ; Nanoparticle ; Materials science ; Polymer ; Amorphous solid ; Chemical engineering ; Self-assembly ; Nanostructure ; Nanotechnology ; Hybrid material ; Chemistry ; Crystallography ; Composite material Pickering emulsions and particle stabilization ; Advanced Polymer Synthesis and Characterization ; Polymer Surface Interaction Studies
Authors: Pallavi Kumari | Yoselin Benitez‐Alfonso | P. Ballone
Source: ChemRxiv (preprint, 2023-04-27)
Field: Materials Science — Biomaterials

Cellulose-Callose Hydrogels: a Computational Exploration of their Structure and Mechanical Properties The accumulation of callose ($\beta$-1,3 glucans) greatly affects plant cell wall physico-mechanical properties and intercellular communication. In this paper, the structural, bonding and mechanical properties of cellulose - callose hydrogel mixtures, consisting of $90$ wt\% water and $10$ wt\% polysaccharide, have been investigated by atomistic molecular dynamics simulations. Systems of this kind have recently been investigated experimentally aiming at gaining insight into the properties underlying callose roles in plant cell walls. The simulation results show that samples of $N=1.5\times 10^6$ atoms and volume $V=(25)^3$ nm$^3$ simulated for $300$ ns provide a qualitatively consistent view of the hydrogel properties, although a quantitative comparison with experiments might require to extend significantly the linear size of the samples and the time scale of the simulation. A complementary set of simulations have been carried out for model samples representing dense cellulose-callose structures, contaminated by or immersed in water. The results provide a valuable microscopic picture for the interpretation of experimental data on cellulose-callose hydrogels, and, in perspective, might help understanding the role of mixing callose and cellulose in critical cell wall structures. All the simulation data provide a tuning and testing ground for the development of coarse-grained models that are required for the systematic investigation of mechanical properties of cellulose, callose and water mixtures. Callose ; Cellulose ; Self-healing hydrogels ; Materials science ; Polysaccharide ; Molecular dynamics ; Chemical engineering ; Cell wall ; Composite material ; Biological system ; Chemistry ; Polymer chemistry ; Organic chemistry ; Computational chemistry ; Biochemistry Advanced Cellulose Research Studies ; Polysaccharides and Plant Cell Walls ; Polysaccharides Composition and Applications
Authors: Ayobami Damilare Adisa | Patience Folashade Olabinri | Adejoke Tolulope Oyedeji | Fiyinfoluwa Demilade Ojeniyi | James Busayo Agboola | Muinat Fehintola Zubair | Gbadebo Joshua Ojo | Leonard Ona Ehigie | Adeola Folasade Ehigie
Source:  (article, 2023-09-03)
Field: Materials Science — Biomaterials

In silico and In vivo Studies of Calotropis procera leaf and root extracts on Mitochondrial-Related parameters in Wistar Rats Drugs targeting Mitochondrial Membrane Permeability Transition (MMPT) pore opening are of great interest for conditions arising from apoptosis dysregulation. This study investigate MMPT pore inducing effect of Calotropis procera leaves and root extracts on mitochondrial-related parameters in the liver of healthy male Wistar rats. Extraction was done by standard methods, using Ethylacetate and Butanol solvent. Fifty–two rats weighing between 130 g - 150 g were divided into thirteen groups (n=4). Group 1 received distilled water, other groups were administered ethylacetate leaf extract (ELE), butanol leaf extract (BLE), ethylacetate root extract (ERE) and butanol root extracts (BRE). Liver Mitochondrial pore opening, mitochondrial ATPase activity and lipid peroxidation were assessed spectrophotometrically, while the interaction between human Cyclophilin D (a pore activating protein with PDB ID: 2BIT) and identified phytochemicals of Calotropis procera leaves and roots extracts were studied In-silico. Varying concentrations of the extracts induced MMPT pore opening by 6.6, 7.4 and 5.9 folds for BLE and 10.2, 7.3 and 6.4 folds for ELE at 40, 50 and 60 mg/100g bw respectively when compared with control group. Root extracts showed significant MMPT pore opening with a fold increase of 12.2, 10.1 and 20.4 for BRE and 11.37, 11.84, for ERE at at 40 , 50 and 60 mg/100g bw respectively. BLE, BRE, ELE and ERE showed increase in ATPase activities with respect to the control group. Malondialdehyde (MDA) levels as an indication of lipid peroxidation increased significantly when compared with control. Molecular docking and simulation showed the existence of stable interactions between human Cyclophilin D with phytochemicals of Calotropis procera with 2‶-Oxovoruscharin having highest binding affinity of -7.9 kcal/mol. C. procera has potential for therapeutic use for the treatment of disorders related to derangement of Calotropis procera ; Lipid peroxidation ; Biology ; Malondialdehyde ; Procera ; Pharmacology ; Biochemistry ; Traditional medicine ; Antioxidant ; Botany ; Medicine Phytochemistry and Bioactive Compounds ; Vitamin C and Antioxidants Research ; Natural Antidiabetic Agents Studies
Authors: Sriteja Mantha | Alec Glisman | Decai Yu | Eric P. Wasserman | Scott A. Backer | Zhen‐Gang Wang
Source: arXiv (Cornell University) (preprint, 2023-11-19)
Field: Chemistry — Physical and Theoretical Chemistry

Adsorption isotherm and mechanism of $\mathrm{Ca^{2+}}$ binding to polyelectrolyte Polyelectrolytes, such as polyacrylic acid (PAA), can effectively mitigate $\mathrm{CaCO_3}$ scale formation. Despite their success as antiscalants, the underlying mechanism of $\mathrm{Ca^{2+}}$ binding to polyelectrolyte chains remains unresolved. Through all-atom molecular dynamics simulations, we construct an adsorption isotherm of $\mathrm{Ca^{2+}}$ binding to sodium polyacrylate ($\mathrm{NaPAA}$) and investigate the associated binding mechanism. We find that the number of calcium ions adsorbed $[\mathrm{Ca^{2+}_{ads}}]$ to the polymer saturates at moderately high concentrations of free calcium ions $[\mathrm{Ca^{2+}_{aq}}]$ in the solution. This saturation value is intricately connected with the binding modes accessible to $\mathrm{Ca^{2+}}$ ions when they bind to the polyelectrolyte chain. We identify two dominant binding modes: the first involves binding to at most two carboxylate oxygens on a polyacrylate chain, and the second, termed the high binding mode, involves binding to four or more carboxylate oxygens. As the concentration of free calcium ions $[\mathrm{Ca^{2+}_{aq}}]$ increases from low to moderate levels, the polyelectrolyte chain undergoes a conformational transition from an extended coil to a hairpin-like structure, enhancing the accessibility to the high binding mode. At moderate concentrations of $[\mathrm{Ca^{2+}_{aq}}]$, the high binding mode accounts for at least a third of all binding events. The chain's conformational change and its consequent access to the high binding mode is found to increase the overall $\mathrm{Ca^{2+}}$ ion binding capacity of the polyelectrolyte chain. Polyelectrolyte ; Carboxylate ; Crystallography ; Polyacrylic acid ; Adsorption ; Conformational change ; Chemistry ; Ion ; Polymer ; Stereochemistry ; Physical chemistry ; Organic chemistry Electrostatics and Colloid Interactions ; Polymer Surface Interaction Studies ; Surfactants and Colloidal Systems
Authors: Fabian A. Freire-Moschovitis | Roberto Rizzato | Anton Pershin | Moritz R. Schepp | Robin D. Allert | Lina M. Todenhagen | Martin S. Brandt | Ádám Gali | Dominik Bucher
Source: arXiv (Cornell University) (preprint, 2023-01-12)
Field: Materials Science — Materials Chemistry

The Role of Electrolytes in the Relaxation of Near-Surface Spin Defects in Diamond Quantum sensing with spin defects in diamond, such as the nitrogen-vacancy (NV) center, enables the detection of various chemical species on the nanoscale. Molecules or ions with unpaired electronic spins are typically probed by their influence on the NV center's spin relaxation. Whereas it is well-known that paramagnetic ions reduce the NV center's relaxation time ($T_1$), here we report on the opposite effect for diamagnetic ions. We demonstrate that millimolar concentrations of aqueous diamagnetic electrolyte solutions increase the $T_1$ time of near-surface NV center ensembles compared to pure water. To elucidate the underlying mechanism of this surprising effect, single and double quantum NV experiments are performed, which indicate a reduction of magnetic and electric noise in the presence of diamagnetic electrolytes. In combination with ab initio simulations, we propose that a change in the interfacial band bending due to the formation of an electric double layer leads to a stabilization of fluctuating charges at the interface of an oxidized diamond. This work not only helps to understand noise sources in quantum systems but could also broaden the application space of quantum sensors towards electrolyte sensing in cell biology, neuroscience and electrochemistry. Diamagnetism ; Paramagnetism ; Chemical physics ; Diamond ; Relaxation (psychology) ; Spins ; Ion ; Electrolyte ; Condensed matter physics ; Chemistry ; Materials science ; Physics ; Magnetic field ; Physical chemistry ; Electrode Diamond and Carbon-based Materials Research ; Electronic and Structural Properties of Oxides ; Force Microscopy Techniques and Applications
Authors: Yijing Zhang | Yue Sun | Jingya Nan | Fusheng Yang | Zihao Wang | Yuxi Li | Chuchu Wang | Fuxiang Chu | Yupeng Liu | Chunpeng Wang
Source: Research Square (preprint, 2023-09-26)
Field: Materials Science — Electronic, Optical and Magnetic Materials

In situ polymerization of hydrogel electrolyte on electrode enabling the flexible all-hydrogel supercapacitors with low-temperature adaptability <title>Abstract</title> All-hydrogel supercapacitors are emerging as promising power sources for next-generation wearable electronics due to their intrinsically mechanical flexibility, eco-friendliness, and enhanced safety. However, the insufficient interfacial adhesion between electrode and electrolyte and the frozen hydrogel matrices at subzero temperatures largely limit the practical applications of all-hydrogel supercapacitors. Here, we report an all-hydrogel supercapacitor with robust interfacial contact and anti-freezing property, which is fabricated by in situ polymerizing hydrogel electrolyte onto hydrogel electrode. The robust interfacial adhesion is developed by the synergistic effect of tough hydrogel matrix and topological entanglements. Meanwhile, the incorporation of ZnCl<sub>2</sub> in the hydrogel electrolyte prevents water solvents from freezing and endows the all-hydrogel supercapacitor with mechanical flexibility and fatigue resistance across a wide temperature range of 20°C to − 60°C. Such all-hydrogel supercapacitor demonstrates satisfactory low-temperature electrochemical performance, delivering high energy density of 11 mWh cm<sup>–2</sup> and excellent cycling stability with capacitance retention of 99% over 5000 cycles at − 40°C. Notably, the fabricated all-hydrogel supercapacitor can endure dynamic deformations and operate well under 2000 tension cycles even at − 40°C, without delamination and electrochemical failure. This work offers a promising strategy for flexible energy storage devices with low-temperature adaptability. Supercapacitor ; Materials science ; Electrolyte ; Self-healing hydrogels ; Electrode ; Energy storage ; Capacitance ; In situ polymerization ; Nanotechnology ; Polymerization ; Composite material ; Polymer ; Polymer chemistry ; Chemistry Supercapacitor Materials and Fabrication ; Advanced Sensor and Energy Harvesting Materials ; Electrospun Nanofibers in Biomedical Applications
Authors: Marius Kadek | Baokai Wang | Marc Joosten | Wei-Chi Chiu | François Mairesse | Michal Repiský | Kenneth Ruud | Arun Bansil
Source: arXiv (Cornell University) (preprint, 2023-01-31)
Field: Materials Science — Materials Chemistry

Band structures and $\mathbb{Z}_2$ invariants of two-dimensional transition metal dichalcogenide monolayers from fully-relativistic Dirac-Kohn-Sham theory using Gaussian-type orbitals Two-dimensional (2D) materials exhibit a wide range of remarkable phenomena, many of which owe their existence to the relativistic spin-orbit coupling (SOC) effects. To understand and predict properties of materials containing heavy elements, such as the transition-metal dichalcogenides (TMDs), relativistic effects must be taken into account in first-principles calculations. We present an all-electron method based on the four-component Dirac Hamiltonian and Gaussian-type orbitals (GTOs) that overcomes complications associated with linear dependencies and ill-conditioned matrices that arise when diffuse functions are included in the basis. Until now, there has been no systematic study of the convergence of GTO basis sets for periodic solids either at the nonrelativistic or the relativistic level. Here we provide such a study of relativistic band structures of the 2D TMDs in the hexagonal (2H), tetragonal (1T), and distorted tetragonal (1T') structures, along with a discussion of their SOC-driven properties (Rashba splitting and $\mathbb{Z}_2$ topological invariants). We demonstrate the viability of our approach even when large basis sets with multiple basis functions involving various valence orbitals (denoted triple- and quadruple-$ζ$) are used in the relativistic regime. Our method does not require the use of pseudopotentials and provides access to all electronic states within the same framework. Our study paves the way for direct studies of material properties, such as the parameters in spin Hamiltonians, that depend heavily on the electron density near atomic nuclei where relativistic and SOC effects are the strongest. Relativistic quantum chemistry ; Atomic orbital ; Hamiltonian (control theory) ; Physics ; Tetragonal crystal system ; Electronic structure ; Electronic band structure ; Quantum mechanics ; Density functional theory ; Basis function ; Dirac equation ; Condensed matter physics ; Electron ; Mathematics 2D Materials and Applications ; Topological Materials and Phenomena ; Advanced Chemical Physics Studies
Authors: Adrián D. Boccardo | Mei Song Tong | S.B. Leen | D. Tourret | Javier Segurado
Source: arXiv (Cornell University) (preprint, 2023-06-07)
Field: Materials Science — Materials Chemistry

Efficiency and accuracy of GPU-parallelized Fourier spectral methods for solving phase-field models Phase-field models are widely employed to simulate microstructure evolution during processes such as solidification or heat treatment. The resulting partial differential equations, often strongly coupled together, may be solved by a broad range of numerical methods, but this often results in a high computational cost, which calls for advanced numerical methods to accelerate their resolution. Here, we quantitatively test the efficiency and accuracy of semi-implicit Fourier spectral-based methods, implemented in Python programming language and parallelized on a graphics processing unit (GPU), for solving a phase-field model coupling Cahn-Hilliard and Allen-Cahn equations. We compare computational performance and accuracy with a standard explicit finite difference (FD) implementation with similar GPU parallelization on the same hardware. For a similar spatial discretization, the semi-implicit Fourier spectral (FS) solvers outperform the FD resolution as soon as the time step can be taken 5 to 6 times higher than afforded for the stability of the FD scheme. The accuracy of the FS methods also remains excellent even for coarse grids, while that of FD deteriorates significantly. Therefore, for an equivalent level of accuracy, semi-implicit FS methods severely outperform explicit FD, by up to 4 orders of magnitude, as they allow much coarser spatial and temporal discretization. Discretization ; Graphics processing unit ; Computer science ; Spectral method ; Python (programming language) ; Computational science ; Fast Fourier transform ; Finite difference ; Algorithm ; Fourier transform ; Pseudo-spectral method ; Parallel computing ; Graphics ; CUDA ; Partial differential equation ; Applied mathematics ; Mathematics ; Fourier analysis ; Mathematical analysis ; Computer graphics (images) Solidification and crystal growth phenomena ; Aluminum Alloy Microstructure Properties ; Magnetic Properties and Applications
Authors: Maxime Vassaux
Source: arXiv (Cornell University) (preprint, 2023-12-20)
Field: Materials Science — Biomaterials

Heterogeneous structure and dynamics of water in a hydrated collagen microfibril Collagen type I is well-known for its outstanding mechanical properties which it inherits from its hierarchical structure. Collagen type I fibrils may be viewed as an heterogeneous material made of protein, macromolecules (such as glycosaminoglycans and proteoglycans) and water. Water content modulates the properties of these heterofibrils. Yet, the properties of water and the fine interactions of water with the protein constituent of these nanocomposites have only received limited attention. Here, we propose to model collagen type I fibrils as an hydrated structure made of tropocollagen molecules assembled in a microfibril crystal. We perform large-scale all-atom molecular dynamics simulations of the hydration of collagen fibrils beyond the onset of disassembly. We found that the structural and dynamic properties of water vary strongly with the level of hydration of the microfibril. More importantly, we found that the properties vary spatially within the 67 nm D-spacing periodic structure. Alteration of the structural and dynamical properties of the collagen microfibril occur first in the gap region. Overall, we identify that the change in the role of water molecules from glue to lubricant between tropocollagen molecules arises around 100% hydration while the microfibril begins to disassemble beyond 130% water content. Our findings are supported by a decrease in hydrogen bonding, recovery of bulk water properties and amorphisation of the tropocollagen molecules packing. Our simulations reveal the structure and dynamics of hydrated collagen fibrils with unprecedented spatial resolution from physiological conditions to disassembly. Beyond the process of self-assembly and the emergence of mechanical properties of collagen type I fibrils, our results may also provide new insights in mineralization of collagen fibrils. Microfibril ; Biomineralization ; Macromolecule ; Crystal structure ; Molecular dynamics ; Chemistry ; Biophysics ; Chemical physics ; Type I collagen ; Crystal (programming language) ; Chemical engineering ; Materials science ; Cellulose ; Crystallography ; Computational chemistry ; Biochemistry Collagen: Extraction and Characterization
Authors: Victor Kwan | Pranav Ballaney | Titiksha Titiksha | Styliani Consta
Source: ChemRxiv (preprint, 2023-05-02)
Field: Chemistry — Spectroscopy

Limitations of atomistic molecular dynamics to reveal ejection of proteins from charged nanodroplets Atomistic molecular dynamics (MD) is frequently used to unravel the mechanisms of macroion release from electrosprayed droplets. However, atomistic MD is currently feasible for only the smallest window of droplet sizes appearing at the end steps of a droplet's lifetime. The relevance of the observations made to the actual droplet evolution, which is much longer that the simulated sizes, has not been addressed yet in the literature. Here, we perform a systematic study of desolvation mechanisms of poly(ethylene glycol) (PEG), protonated peptides of different compositions and proteins in order to (a) obtain insight into the charging mechanism of macromolecules in larger droplets than those that are currently amenable to atomistic MD, and (b) examine whether currently used atomistic modeling can establish the extrusion mechanism of proteins from droplets. To mimic larger droplets that are not amenable to MD modeling, we scale down the systems, by simulating a large droplet size relative to the macromolecule. MD of PEG charging reveals that above a critical droplet size, ions are available near the backbone of the macromolecule, but charging occurs only transiently by transfer of ions from the solvent to the macroion, while below the critical size, the capture of the ion from PEG has a lifetime sufficiently long for extrusion of a charged PEG from the aqueous droplet. This is the first report of the role of droplet curvature in the relation between macroion conformation and charging. Simulations of peptides with high degree of hydrophobicity show that partial extrusion of a peptide from the droplet surface is rare relative to desolvation by drying-out. Differently from what has been presented in the literature we argue that atomistic MD simulations have not sufficiently established extrusion mechanism of proteins from droplets and their charging mechanism. We also argue that release of highly charged proteins can occur at an earlier stage of a droplet's lifetime than predicted by atomistic MD. In this earlier stage, we emphasize the key role of jets emanating from a droplet at the point of charge-induced instability in the release of proteins. Molecular dynamics ; Chemical physics ; Macromolecule ; Ethylene glycol ; Chemistry ; Extrusion ; Ion ; PEG ratio ; Aqueous solution ; Nanotechnology ; Materials science ; Computational chemistry ; Physical chemistry ; Organic chemistry Mass Spectrometry Techniques and Applications ; Electrohydrodynamics and Fluid Dynamics ; Microfluidic and Capillary Electrophoresis Applications