jablonkagroup/rise_ai_scientists huggingface dataset:
Authors: Matthew M. Graham | Alexandre H. Thiéry | Alexandros Beskos
Source: arXiv (Cornell University) (preprint, 2019-12-06)
Field: Chemistry — Spectroscopy

Manifold Markov chain Monte Carlo methods for Bayesian inference in diffusion models Bayesian inference for nonlinear diffusions, observed at discrete times, is a challenging task that has prompted the development of a number of algorithms, mainly within the computational statistics community. We propose a new direction, and accompanying methodology, borrowing ideas from statistical physics and computational chemistry, for inferring the posterior distribution of latent diffusion paths and model parameters, given observations of the process. Joint configurations of the underlying process noise and of parameters, mapping onto diffusion paths consistent with observations, form an implicitly defined manifold. Then, by making use of a constrained Hamiltonian Monte Carlo algorithm on the embedded manifold, we are able to perform computationally efficient inference for a class of discretely observed diffusion models. Critically, in contrast with other approaches proposed in the literature, our methodology is highly automated, requiring minimal user intervention and applying alike in a range of settings, including: elliptic or hypo-elliptic systems; observations with or without noise; linear or non-linear observation operators. Exploiting Markovianity, we propose a variant of the method with complexity that scales linearly in the resolution of path discretisation and the number of observation times. Python code reproducing the results is available at https://doi.org/10.5281/zenodo.5796148 Markov chain Monte Carlo ; Computer science ; Algorithm ; Bayesian inference ; Inference ; Monte Carlo method ; Hybrid Monte Carlo ; Discretization ; Bayesian probability ; Applied mathematics ; Statistical physics ; Mathematics ; Artificial intelligence ; Physics ; Statistics Diffusion Coefficients in Liquids ; Markov Chains and Monte Carlo Methods ; Statistical Methods and Bayesian Inference
Authors: Parisa Shiri | Earl Jon S. Dacanay | Brennan Hagen | Loren G. Kaake
Source: The Journal of Physical Chemistry (article, 2019-01-01)
Field: Materials Science — Polymers and Plastics

Dynamic Charging Mechanism of Organic Electrochemical Devices Revealed with In Situ Infrared Spectroscopy The steps responsible for device charging in organic electrochemical transistors were investigated using in situ infrared spectroscopy. Metal–electrolyte-dielectric–organic semiconductor capacitor structures were fabricated on infrared waveguides and measured using the total internal reflection sampling method. Upon the application of a voltage, charges were induced in the device, creating polaron absorption features in the mid-infrared region. The dynamics of the device charging were investigated by varying the channel length, dielectric layer thickness, and organic semiconductor layer thickness. Device charging was independent of the channel length but depended strongly on the semiconductor and dielectric layer thicknesses, indicating that the movement of ions is the primary determining factor for device charging kinetics. A quantitative model is developed combining an resistor-capacitor (RC) circuit model for the dielectric layer and a mixed ion–carrier diffusion model for the organic semiconductor layer. The model is evaluated against an RC circuit model for electrochemical charging dynamics, which is used in the popular Bernards model. Thickness-dependent dynamics cannot be adequately explained using the RC circuit model. The model presented here is significantly more appropriate for fundamental studies of ion dynamics in pi-conjugated materials. Chemistry ; Semiconductor ; Capacitor ; Organic semiconductor ; Optoelectronics ; Attenuated total reflection ; Infrared spectroscopy ; Dielectric ; Analytical Chemistry (journal) ; Infrared ; Electrolyte ; Electrode ; Materials science ; Voltage ; Optics ; Electrical engineering ; Physical chemistry Conducting polymers and applications ; Organic Electronics and Photovoltaics ; Analytical Chemistry and Sensors
Authors: Christine Peters
Source: RWTH Publications (RWTH Aachen) (article, 2019-01-01)
Field: Chemistry — Analytical Chemistry

Messung von Multikomponentendiffusion in Flüssigkeiten mit Raman-Mikrospektroskopie und Mikrofluidik Diffusion is the rate-limiting mass transport step in many (bio)chemical processes. Diffusion data is therefore necessary to design unit operations, e.g., extraction. However, diffusion data on multicomponent mixtures in liquids are scarce, as diffusion measurements are intrinsically time-consuming and laborious. Also, several measurements are required for one diffusion coefficient matrix in a multicomponent mixture. Microfluidics promises to reduce experiment time and experimental effort, while Raman spectroscopy reduces the number of necessary experiments for multicomponent mixtures. To reduce the measurement effort for diffusion coefficients in multicomponent mixtures, microfluidics and Raman microspectroscopy were combined in this work for the first time for the measurement of diffusion coefficient matrices in multicomponent mixtures: Two liquids of different concentrations co-flow in parallel in a microfluidic H-cell, while changes of concentration due to diffusion are quantified locally using Raman microspectroscopy. From these changes of concentration, the diffusion coefficient matrix is determined in a least squares procedure using a convection-diffusion-model. Thereby, diffusion coefficient matrices can be determined from a single experiment, while the known initial concentrations together with quantitative Raman spectroscopy spare additional calibration measurements. The experiment takes less than 1h and the sample consumption is below 6mL.The developed method to determine diffusion coefficients was validated for binary and ternary systems. Additionally, new diffusion data was measured for a binary, a ternary and a quaternary system. Two and three experiments are sufficient to determine diffusion coefficient matrices with accuracy and precision for ternary and quaternary systems respectively. Systems used for validation agree with literature data. Thus, diffusion coefficient matrices of multicomponent mixture can be provided with small effort and in short time to enable the design of unit operations. Raman microspectroscopy ; Microfluidics ; Raman spectroscopy ; Diffusion ; Materials science ; Nanotechnology ; Chemistry ; Optics ; Physics ; Thermodynamics Spectroscopy and Chemometric Analyses ; Spectroscopy Techniques in Biomedical and Chemical Research
Authors: Ryan T. Woodall | David A. Hormuth | Michael Abdelmalik | Chengyue Wu | Xinzeng Feng | William Phillips | Ande Bao | Thomas J.R. Hughes | Andrew Brenner | Thomas E. Yankeelov
Source: Neuro-Oncology (article, 2019-11-01)
Field: Materials Science — Biomaterials

SCIDOT-38. DEVELOPMENT OF AN IMAGE-INFORMED MATHEMATICAL MODEL OF CONVECTION-ENHANCED DELIVERY OF NANOLIPOSOMES FOR INDIVIDUAL PATIENTS Abstract 186-Rhenium nanoliposomes (RNL) are an experimental theranostic being investigated for the treatment of recurrent Glioblastoma. While traditional external beam therapy exposures healthy tissue to radiation, RNL has the potential to deliver extremely large doses (&gt; 2000 Gy) of localized radiation, minimally exposing surrounding tissue. RNL is delivered directly to the malignancy by convection-enhanced delivery (CED) via intracranial catheter. For this reason, accurate and precise delivery of RNL to the target region is an imperative. While models of CED for molecular agents exist, we know of no such models for CED of liposomal nanoparticles. To that end, we are developing a patient-specific advection-diffusion model of RNL delivery and distribution, informed by pre-delivery quantitative magnetic resonance imaging (MRI) parameters, and validated by intra-delivery single-photon emission computed tomography (SPECT). Apparent liposome diffusivity and interstitial hydraulic conductivity are spatially informed by diffusion weighted MRI, while the clearance of interstitial fluid is spatially informed by the T1 enhancement ratio after contrast agent delivery. The model output is compared to SPECT images at two time points, acquired mid-way through and immediately following the RNL infusion. At the time of submission, the model has been calibrated by patient-specific data to match the spatiotemporal distribution of RNL in four patients. After calibration, the concordance correlation coefficient between the model and SPECT measurements was 0.80 +/- 0.23 mid-way through the infusion volume, and 0.86 +/- 0.14 immediately post-infusion. The DICE coefficient between the modeled delivery volume and measured delivery volume was 0.86 +/- 0.10 mid-way through the infusion volume, and 0.81 +/- 0.14 immediately post-infusion (reported as mean +/- 95% confidence intervals). These results provide preliminary evidence that the model can capture the spatiotemporal distribution of RNL during and after delivery, and may enable physicians to better plan CED procedures for liposomal nanotherapeutics in the future. Nuclear medicine ; Magnetic resonance imaging ; Biomedical engineering ; Materials science ; Medicine ; Radiology Nanoparticle-Based Drug Delivery ; Nanoplatforms for cancer theranostics ; Glioma Diagnosis and Treatment
Authors: Kerry Jean Lee
Source: ODU Digital Commons (Old Dominion University) (article, 2019-05-13)
Field: Materials Science — Materials Chemistry

Design of <i>In Vivo</i> Assays for Study of Transport, Biocompatibility and Toxicity of Nanoparticles This dissertation focuses on the design of new in vivo assays for study of transport, biocompatibility and toxicity of nanoparticles (NPs) in zebrafish embryos. We synthesized and purified spherical silver (Ag) NPs with diameters, ranging from 12 to 95 nm, that are stable (non-aggregated) in egg-water media. We developed new imaging approaches to characterize the sizes of single Ag NPs in zebrafish embryos at nanometer resolution by measuring their size-dependent plasmonic spectra and scattering intensity using dark-field optical microscopy and spectroscopy (DFOMS). We used single Ag NPs because they exhibit the high quantum yield (QY) of Rayleigh scattering and resist photobleaching and blinking, allowing to be continuously monitored in vivo for any desired amount of time. These unique optical properties make them better than traditional imaging probes, such as fluorescence probes (e.g., fluorophores and semiconductor quantum dots), that are currently used for in vivo imaging and widely used in life science. With no need of fluorescence excitation, Ag NPs can be used to monitor transport in a living in vivo system and effectively avoids auto-fluorescence of the living organism, allowing us to monitor it in real-time in the developing embryo. Using different properties of Ag NPs, size-dependent optical properties and charge-dependent surface properties, we studied transport and toxicity in living embryos in real-time for better understanding of biocompatibility of NPs in a living in vivo model system. Using Ag NPs, we continuously imaged nano-environments of developing zebrafish embryos for hours and discovered their transport patterns through the chorion and into the chorion space of the different stages of embryos. We demonstrated that the different types of Ag NPs caused a wide variety of deformities and caused an increase in death, and both in a concentration dependent manner in living zebrafish embryos. This determined that zebrafish embryos are a powerful in vivo assay to use to study the transport, biocompatibility and toxicity of nanomaterials. Biocompatibility ; Photobleaching ; In vivo ; Nanotechnology ; Nanoparticle ; Materials science ; Preclinical imaging ; Fluorescence ; Biophysics ; Silver nanoparticle ; Zebrafish ; Chemistry ; Optics ; Biology ; Physics ; Biochemistry Nanoparticles: synthesis and applications
Authors: Izabel Cristina Medeiros Costa
Source: SPIRE - Sciences Po Institutional REpository (preprint, 2019-02-28)
Field: Chemistry — Inorganic Chemistry

Adsorption/diffusion interplay in hierarchical zeolites : understanding the role of external surface and additional porosity The performance of xylene separation processes using nanoporous adsorbents is related to both the transport and selectivity properties of the used faujasite zeolites (BaX). Conventional zeolites exhibit a large volume of micropores and a good selectivity to paraxylene (px). However, intracrystalline diffusion is a slow process which limits the efficiency of the zeolites. Therefore, the use of hierarchical zeolites has been proposed as an alternative to improve transport properties by the introduction of an additional porous network. In this thesis, two types of BaX hierarchical zeolites are considered: Nanoparticles aggregates (NA - aggregates of small particles with mesopores between them) and Layer-like zeolite (LL - array of zeolite layers, with the presence of inter and intra-layers mesopores). In order to better understand the role played by the external surface and by the additional porosity in hierarchical zeolites (NA and LL), these zeolites were characterized in terms of quantity and quality of the external surface by the application of different characterization techniques (X-ray diffraction, N2 adsorption, porosimetry, microscopy, infrared and nuclear magnetic resonance). The xylene adsorption and diffusion were evaluated in gas and liquid phase, by means of thermogravimetry and batch experiments, respectively. Through the experiments in liquid phase, it is noticed that the xylene diffusion in hierarchical zeolites is considerably improved. On the other hand, a significant loss in px-selectivity in hierarchical BaX zeolites is observed compared to conventional BaX zeolites. The study of diffusion in gas phase allowed the identification of surface barriers, which are not present in the liquid phase. This may be an indication that, when the concentration around the surface is large (liquid phase), the passage of molecules across the surface is less/not disturbed. This reinforces the interest of using hierarchical zeolite for xylene separation which is carried out in liquid phase Adsorption ; Porosity ; Diffusion ; Materials science ; Surface diffusion ; Chemical engineering ; Surface (topology) ; Nanotechnology ; Chemical physics ; Chemistry ; Thermodynamics ; Composite material ; Engineering ; Physical chemistry ; Physics ; Geometry ; Mathematics Zeolite Catalysis and Synthesis ; Catalysis and Hydrodesulfurization Studies
Authors: Sayoni Ray
Source: eScholarship (California Digital Library) (article, 2019-01-01)
Field: Materials Science — Biomaterials

Cancer Nano-Theranostics with High Contrast MRI One of the holy grails in cancer therapy is to simultaneously image and deliver drugs to the tumor site. The first part of the thesis has developed new ideas in cancer theranostics and the second part is about the development of a novel contrast agent for risk-free imaging of the tumor. In the first project of the thesis, I have discussed the development of a liposome-based cargo delivery strategy that can simultaneously monitor alternating magnetic field–induced drug release by observing the change in MRI relaxation parameter R1, and the location and condition of liposomal site (such as tumor) from MRI parameter R2. However, the loading of a contrast agent in liposomes generally results in poor contrast and suffers from various artifacts in in vivo experiments, compared to the use of free contrast agent. Thus, the second project of my work in this part demonstrates the effective filtering of artifacts and contrast enhancement to obtain high quality sensitive imaging of the tumor site in a mouse model using paramagnetic liposomes, a novel pulsing sequence in active-feedback MRI, and robust data analysis. The second part of my work is about using a self-replicating viral-RNA molecule derived from Nodamura, an insect virus, to express and amplify ferritin, leading to increased iron content of the cells in the form of ferrihydrite that acts as a novel contrast agent. In summary, my thesis is about the development of cancer theranostics and a novel contrast agent. In the last part of the thesis, I have reviewed the current development of rapidly growing state of the art magnetic resonance cancer theranostics for commonly used polymer-based nanovehicles. Liposome ; Contrast (vision) ; Drug delivery ; Cancer ; In vivo ; Biomedical engineering ; Contrast enhancement ; Nanotechnology ; Computer science ; Magnetic resonance imaging ; Materials science ; Medical physics ; Nuclear magnetic resonance ; Chemistry ; Medicine ; Artificial intelligence ; Radiology ; Physics ; Biology Nanoparticle-Based Drug Delivery ; Advanced Biosensing Techniques and Applications
Authors: Nat Sakol
Source: Institutional Repositories DataBase (IRDB) (article, 2019-03-25)
Field: Chemistry — Spectroscopy

NMR study of biomolecular localization in cells by the paramagnetic relaxation Paramagnetism ; Chemistry ; Relaxation (psychology) ; Nuclear magnetic resonance ; Physics ; Condensed matter physics ; Biology ; Neuroscience Advanced NMR Techniques and Applications ; Advanced MRI Techniques and Applications ; NMR spectroscopy and applications
Authors: ハスツチ ノビトリ
Source: Kyushu University Institutional Repository (QIR) (Kyushu University) (article, 2019-09-25)
Field: Materials Science — Biomaterials

Functional Nanocellulose from Oil Palm Empty Fruit Bunches Pulp The use of agricultural residues as inexpensive raw materials to produce highvalue natural nanomaterials such as nanocellulose is aligned with the concept of Sustainable Development Goals (SDGs) by pioneering its promising functions in several applications.Nanocellulose derived from oil palm empty fruit bunches (OPEFB) pulp has been successfully extracted by hydrochloric acid hydrolysis and 2,2,6,6-Tetramethylpiperidine 1-oxyl (TEMPO) -mediated oxidation, respectively, affording cellulose nanocrystals (CNCs) and TEMPO-oxidized cellulose nanofibers (TOCNs).The CNC suspensions prepared from OPEFB by HCl hydrolysis remained stable without any sedimentation over 6 months.The OPEFB-derived CNCs exhibited high aspect ratios and superior thermal stability compared with those of woody CNCs.Very fine TOCNs in 3-nm thickness obtained from OPEFB pulps possessed high aspect ratios rather than 40 with various contents of carboxylates (1.0-1.5 mmol/g-TOCN), and showed good thermal stability.Furthermore, highly-charged TOCNs from OPEFB were very effective in extractive fermentation to enhance butanol production.TOCNs were successfully applied to extractive fermentation using Clostridium saccharoperbutylacetonicum N1-4 as a butanol-producing strain.The butanol yield from free and immobilized cells remarkably increased in the presence of OPEFB-derived TOCNs.In the immobilized cell method, crosslinking of anionic carboxylate groups of TOCNs and alginate via Ca 2+ ions to form alginate beads induced favorable 3-D networks for cell entrapment, and possibly provided better microenvironment for bacterial growth.The combination of OPEFB-derived TOCNs and alginate eventually yielded the highest total butanol production up to 37 g/L-broth. Nanocellulose ; Palm oil ; Pulp (tooth) ; Pulp and paper industry ; Palm ; Bunches ; Cellulose ; Horticulture ; Botany ; Chemistry ; Food science ; Biology ; Engineering ; Physics Advanced Cellulose Research Studies ; Nanocomposite Films for Food Packaging ; Material Properties and Processing
Authors: Jennifer A Glancy
Source: eScholarship (California Digital Library) (article, 2019-01-01)
Field: Materials Science — Materials Chemistry

Confirmation of Photoacidic Quantum Dots Using Electrochemical Impedance Spectroscopy This thesis describes the first demonstration of a quantum dot photoacid. Photoacids are a class of molecules with a protic bond that is weakened upon photo-excitation. CdSe quantum dots were synthesized and were made to have mixed-ligand surfaces with a majority of water-solubilizing sulfonate functional groups and fewer acidic electron-donor functional groups, notably 4-mercaptophenol (MPh). Sulfonate groups are very acidic and therefore remain charged over a wide range of pH values. Through judicious choice of synthesis and ligand-exchange conditions, water-solubilizing 2-mercaptoethanesulfonate (MES) was introduced in addition to an equal concentration of protic and dipolar MPh groups. The electronic states of surface-bound MPh groups are such that they can serve as electron-transfer donors to excited-state CdSe quantum dots. The challenge to characterize the photoacidity of this class of chromophores is that the charge-separated CdSe– and MPh+ state does not efficiently emit photons. Therefore, a recently developed electrochemical impedance spectroscopy technique was studied in great detail to understand the cause of observed changes in impedance and then utilized to definitively demonstrate that this new class of quantum dot dyes were photoacidic. This light-driven energy conversion process is uniquely suited to convert light into ionic power, which can be used for direct desalination of saltwater. Quantum dot ; Excited state ; Chemistry ; Sulfonate ; Chromophore ; Dielectric spectroscopy ; Photochemistry ; Electrochemistry ; Chemical physics ; Nanotechnology ; Materials science ; Atomic physics ; Physics ; Physical chemistry ; Electrode ; Organic chemistry Quantum Dots Synthesis And Properties ; TiO2 Photocatalysis and Solar Cells ; Electrochemical Analysis and Applications