scholarly journals Coupling of Charge Regulation and Conformational Equilibria in Linear Weak Polyelectrolytes: Treatment of Long-Range Interactions via Effective Short-Ranged and pH-Dependent Interaction Parameters

Polymers ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 811 ◽  
Author(s):  
Pablo Blanco ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Josep Garcés
Keyword(s):  
Long Range ◽  
Ph Dependence ◽  
Effective Interaction ◽  
Interaction Parameters ◽  
Computational Time ◽  
Physical Parameters ◽  
Wide Range ◽  
Conformational Equilibria ◽  
Ph Dependent ◽  
Weak Polyelectrolytes

The classical Rotational Isomeric State (RIS) model, originally proposed by Flory, has been used to rationalize a wide range of physicochemical properties of neutral polymers. However, many weak polyelectrolytes of interest are able to regulate their charge depending on the conformational state of the bonds. Recently, it has been shown that the RIS model can be coupled with the Site Binding (SB) model, for which the ionizable sites can adopt two states: protonated or deprotonated. The resulting combined scheme, the SBRIS model, allows for analyzing ionization and conformational equilibria on the same foot. In the present work, this approach is extended to include pH-dependent electrostatic Long-Range (LR) interactions, ubiquitous in weak polyelectrolytes at moderate and low ionic strengths. With this aim, the original LR interactions are taken into account by defining effective Short-Range (SR) and pH-dependent parameters, such as effective microscopic protonation constants and rotational bond energies. The new parameters are systematically calculated using variational methods. The machinery of statistical mechanics for SR interactions, including the powerful and fast transfer matrix methods, can then be applied. The resulting technique, which we will refer to as the Local Effective Interaction Parameters (LEIP) method, is illustrated with a minimal model of a flexible linear polyelectrolyte containing only one type of rotating bond. LEIP reproduces very well the pH dependence of the degree of protonation and bond probabilities obtained by semi-grand canonical Monte Carlo simulations, where LR interactions are explicitly taken into account. The reduction in the computational time in several orders of magnitude suggests that the LEIP technique could be useful in a range of areas involving linear weak polyelectrolytes, allowing direct fitting of the relevant physical parameters to the experimental quantities.

scholarly journals Coupling of Charge Regulation and Conformational Equilibria in Linear Weak Polyelectrolytes: Treatment of Long Range Interactions via Effective Short-Ranged and pH-Dependent Interaction Parameters

2018 ◽  
Author(s):  
Pablo M. Blanco ◽  
Sergio Madurga ◽  
Francesc Mas ◽  
Josep L. Garcés
Keyword(s):  
Long Range ◽  
Ph Dependence ◽  
Effective Interaction ◽  
Interaction Parameters ◽  
Computational Time ◽  
Charge Regulation ◽  
Wide Range ◽  
Conformational Equilibria ◽  
Ph Dependent ◽  
Weak Polyelectrolytes

The classical Rotational Isomeric State (RIS) model, originally proposed by Flory, has been used to rationalize a wide range of physicochemical properties of neutral polymers. However, many weak polyelectrolytes of interest are able to regulate their charge depending on the conformational state of the bonds. Recently, it has been shown that the RIS model can be coupled with the Site Binding (SB) model, for which the ionizable sites can adopt two states: protonated or deprotonated. The resulting combined scheme, the SBRIS model, allows to analyse ionization and conformational equilibria on the same foot. In the present work this approach is extended to include pH-dependent electrostatic Long Range (LR) interactions, ubiquitous in weak polyelectrolytes at moderate and low ionic strengths. With this aim the original LR interactions are taken into account by defining effective Short Range (SR) and pH-dependent parameters, such as effective microscopic protonation constants and rotational bond energies. The new parameters are systematically calculated using variational methods. The machinery of statistical mechanics for SR interactions, including the powerful and fast transfer matrix methods, can then be applied. The resulting technique, to which we will refer as Local Effective Interaction Parameters (LEIP) method, is illustrated with a minimal model of a flexible linear polyelectrolyte containing only one type of rotating bonds. LEIP reproduces very well the pH dependence of the degree of protonation and bond probabilities obtained by semi-grand canonical Monte Carlo simulations, where LR interactions are taken explicitly into account. The reduction in the computational time in several orders of magnitude suggests that the LEIP technique could be useful in a range of areas involving linear weak polyelectrolytes, allowing direct fitting of the relevant physical parameters to the experimental quantities.

scholarly journals Numerical Model for the Analysis of Thermal Transients in District Heating Networks

2020 ◽  
Vol 197 ◽  
pp. 01004
Author(s):  
Martina Capone ◽  
Elisa Guelpa ◽  
Vittorio Verda
Keyword(s):  
Carbon Dioxide Emissions ◽  
Renewable Energy Sources ◽  
Management Strategies ◽  
District Heating ◽  
Equivalent Model ◽  
Computational Time ◽  
Physical Parameters ◽  
Thermal Transients ◽  
Proposed Model ◽  
Wide Range

As District Heating (DH) networks are experiencing an evolution towards the so-called 4th generation, there is a need to update the currently used models to take into account the ever-increasing complexity of this technology. Indeed, to further improve the reduction in energy consumption and carbon-dioxide emissions, a wide range of technologies and management strategies are being introduced within district heating, such as a large exploitation of Renewable Energy Sources (RES). As a consequence, thermal transients assume a major importance, posing the need to redefine the relevant physical parameters and to develop a model which accurately describes their behaviour. In this framework, this paper proposes a quantitative analysis of the influence of the pipe heat-capacity on the model. Moreover, an equivalent-model, which is able to take into account the two heat capacities of steel and water in just one equation, is proposed and compared with two commonly used approaches. One of the features of the proposed model is the suitability for application to large networks. To prove its capabilities, an application to the Turin district heating network, which is among the largest systems in Europe, is proposed. Results show significant improvements in terms of accuracy over computational time ratio.

Influence of pH on copper and zinc uptake by soil clays

Soil Research ◽  
1981 ◽  
Vol 19 (3) ◽  
pp. 217 ◽  
Author(s):  
M Maguire ◽  
J Slavek ◽  
I Vimpany ◽  
FR Higginson ◽  
WF Pickering
Keyword(s):  
New South ◽  
Ph Dependence ◽  
Soil Horizons ◽  
Copper And Zinc ◽  
South Wales ◽  
Soil Clays ◽  
Wide Range ◽  
Ph Dependent ◽  
Free Material ◽  
Influence Of Ph

Nine soil clays were isolated from a wide range of soil horizons in New South Wales, and after minerological characterization, the adsorptive behaviour of the NH4+ form of the organic-free material was examined. The amount of copper and zinc sorbed increased with pH and, prior to precipitation of hydroxy species material, differences in pH-dependent capacity were discernible, reflecting differences in clay composition. Uptake at a fixed pH (5) did not always vary with concentration in accordance with Langmuir isotherms. Calculated parameters for amenable systems were similar to those observed by other workers, but capacities at a fixed pH proved to be less informative than pH dependence curves. The implications of the data for availability of the metal ions in the environment have been considered.

scholarly journals pH-Dependent Expression of Periplasmic Proteins and Amino Acid Catabolism in Escherichia coli

2002 ◽  
Vol 184 (15) ◽  
pp. 4246-4258 ◽  
Author(s):  
Lauren M. Stancik ◽  
Dawn M. Stancik ◽  
Brian Schmidt ◽  
D. Michael Barnhart ◽  
Yuliya N. Yoncheva ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Ph Dependence ◽  
Outer Membrane Proteins ◽  
Stress Protein ◽  
Low Ph ◽  
Wide Range ◽  
Periplasmic Proteins ◽  
Ph Dependent ◽  
External Ph

ABSTRACT Escherichia coli grows over a wide range of pHs (pH 4.4 to 9.2), and its own metabolism shifts the external pH toward either extreme, depending on available nutrients and electron acceptors. Responses to pH values across the growth range were examined through two-dimensional electrophoresis (2-D gels) of the proteome and through lac gene fusions. Strain W3110 was grown to early log phase in complex broth buffered at pH 4.9, 6.0, 8.0, or 9.1. 2-D gel analysis revealed the pH dependence of 19 proteins not previously known to be pH dependent. At low pH, several acetate-induced proteins were elevated (LuxS, Tpx, and YfiD), whereas acetate-repressed proteins were lowered (Pta, TnaA, DksA, AroK, and MalE). These responses could be mediated by the reuptake of acetate driven by changes in pH. The amplified proton gradient could also be responsible for the acid induction of the tricarboxylic acid (TCA) enzymes SucB and SucC. In addition to the autoinducer LuxS, low pH induced another potential autoinducer component, the LuxH homolog RibB. pH modulated the expression of several periplasmic and outer membrane proteins: acid induced YcdO and YdiY; base induced OmpA, MalE, and YceI; and either acid or base induced OmpX relative to pH 7. Two pH-dependent periplasmic proteins were redox modulators: Tpx (acid-induced) and DsbA (base-induced). The locus alx, induced in extreme base, was identified as ygjT, whose product is a putative membrane-bound redox modulator. The cytoplasmic superoxide stress protein SodB was induced by acid, possibly in response to increased iron solubility. High pH induced amino acid metabolic enzymes (TnaA and CysK) as well as lac fusions to the genes encoding AstD and GabT. These enzymes participate in arginine and glutamate catabolic pathways that channel carbon into acids instead of producing alkaline amines. Overall, these data are consistent with a model in which E. coli modulates multiple transporters and pathways of amino acid consumption so as to minimize the shift of its external pH toward either acidic or alkaline extreme.

Rationalizing the pH-Activity Response for Escherichia Coli’s Glycinamide Ribonucleotidetransformylase Through Computational Methods

2019 ◽  
Author(s):  
Adrian Roitberg ◽  
Pancham Lal Gupta
Keyword(s):  
Transfer Reaction ◽  
Catalytic Mechanism ◽  
Ph Dependence ◽  
Ph Effects ◽  
Dependent Manner ◽  
E Coli ◽  
Gar Tfase ◽  
Activity Curve ◽  
Ph Dependent ◽  
Formyl Transfer

<div>Human Glycinamide ribonucleotide transformylase (GAR Tfase), a regulatory enzyme in the de novo purine biosynthesis pathway, has been established as an anti-cancer target. GAR Tfase catalyzes the formyl transfer reaction from the folate cofactor to the GAR ligand. In the present work, we study E. coli GAR Tfase, which has high sequence similarity with the human GAR Tfase with most functional residues conserved. E. coli GAR Tfase exhibits structural changes and the binding of ligands that varies with pH which leads to change the rate of the formyl transfer reaction in a pH-dependent manner. Thus, the inclusion of pH becomes essential for the study of its catalytic mechanism. Experimentally, the pH-dependence of the kinetic parameter kcat is measured to evaluate the pH-range of enzymatic activity. However, insufficient information about residues governing the pH-effects on the catalytic activity leads to ambiguous assignments of the general acid and base catalysts and consequently its catalytic mechanism. In the present work, we use pH-replica exchange molecular dynamics (pH-REMD) simulations to study the effects of pH on E. coli GAR Tfase enzyme. We identify the titratable residues governing the pH-dependent conformational changes in the system. Furthermore, we filter out the protonation states which are essential in maintaining the structural integrity, keeping the ligands bound and assisting the catalysis. We reproduce the experimental pH-activity curve by computing the population of key protonation states. Moreover, we provide a detailed description of residues governing the acidic and basic limbs of the pH-activity curve.</div>

pH-Dependent Thermal Stability of Vibrio cholerae L-asparaginase

2019 ◽  
Vol 26 (10) ◽  
pp. 743-750 ◽  
Author(s):  
Remya Radha ◽  
Sathyanarayana N. Gummadi
Keyword(s):  
Vibrio Cholerae ◽  
Conformational Changes ◽  
Kinetic Studies ◽  
Structural Features ◽  
Structure Stability ◽  
Kcal Mole ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
Ph Dependent ◽  
Ph Range

Background:pH is one of the decisive macromolecular properties of proteins that significantly affects enzyme structure, stability and reaction rate. Change in pH may protonate or deprotonate the side group of aminoacid residues in the protein, thereby resulting in changes in chemical and structural features. Hence studies on the kinetics of enzyme deactivation by pH are important for assessing the bio-functionality of industrial enzymes. L-asparaginase is one such important enzyme that has potent applications in cancer therapy and food industry.Objective:The objective of the study is to understand and analyze the influence of pH on deactivation and stability of Vibrio cholerae L-asparaginase.Methods:Kinetic studies were conducted to analyze the effect of pH on stability and deactivation of Vibrio cholerae L-asparaginase. Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) studies have been carried out to understand the pH-dependent conformational changes in the secondary structure of V. cholerae L-asparaginase.Results:The enzyme was found to be least stable at extreme acidic conditions (pH< 4.5) and exhibited a gradual increase in melting temperature from 40 to 81 °C within pH range of 4.0 to 7.0. Thermodynamic properties of protein were estimated and at pH 7.0 the protein exhibited ΔG37of 26.31 kcal mole-1, ΔH of 204.27 kcal mole-1 and ΔS of 574.06 cal mole-1 K-1.Conclusion:The stability and thermodynamic analysis revealed that V. cholerae L-asparaginase was highly stable over a wide range of pH, with the highest stability in the pH range of 5.0–7.0.

scholarly journals A Computational Study on the Role of Parameters for Identification of Thyroid Nodules by Infrared Images (and Comparison with Real Data)

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4459
Author(s):  
José R. González ◽  
Charbel Damião ◽  
Maira Moran ◽  
Cristina A. Pantaleão ◽  
Rubens A. Cruz ◽  
...  
Keyword(s):  
Heat Transfer ◽  
Thyroid Nodules ◽  
Numerical Study ◽  
Computational Study ◽  
Internal Heat ◽  
Heat Transfer Process ◽  
The Body ◽  
Physical Parameters ◽  
Infrared Sensors ◽  
Wide Range

According to experts and medical literature, healthy thyroids and thyroids containing benign nodules tend to be less inflamed and less active than those with malignant nodules. It seems to be a consensus that malignant nodules have more blood veins and more blood circulation. This may be related to the maintenance of the nodule’s heat at a higher level compared with neighboring tissues. If the internal heat modifies the skin radiation, then it could be detected by infrared sensors. The goal of this work is the investigation of the factors that allow this detection, and the possible relation with any pattern referent to nodule malignancy. We aim to consider a wide range of factors, so a great number of numerical simulations of the heat transfer in the region under analysis, based on the Finite Element method, are performed to study the influence of each nodule and patient characteristics on the infrared sensor acquisition. To do so, the protocol for infrared thyroid examination used in our university’s hospital is simulated in the numerical study. This protocol presents two phases. In the first one, the body under observation is in steady state. In the second one, it is submitted to thermal stress (transient state). Both are simulated in order to verify if it is possible (by infrared sensors) to identify different behavior referent to malignant nodules. Moreover, when the simulation indicates possible important aspects, patients with and without similar characteristics are examined to confirm such influences. The results show that the tissues between skin and thyroid, as well as the nodule size, have an influence on superficial temperatures. Other thermal parameters of thyroid nodules show little influence on surface infrared emissions, for instance, those related to the vascularization of the nodule. All details of the physical parameters used in the simulations, characteristics of the real nodules and thermal examinations are publicly available, allowing these simulations to be compared with other types of heat transfer solutions and infrared examination protocols. Among the main contributions of this work, we highlight the simulation of the possible range of parameters, and definition of the simulation approach for mapping the used infrared protocol, promoting the investigation of a possible relation between the heat transfer process and the data obtained by infrared acquisitions.

Structure–property–function relationship of fluorescent conjugated microporous polymers

2021 ◽  
Author(s):  
M. G. Monika Bai ◽  
H. Vignesh Babu ◽  
V. Lakshmi ◽  
M. Rajeswara Rao
Keyword(s):  
Long Range ◽  
Structure Property ◽  
Porous Organic Polymers ◽  
Aggregation Induced Emission ◽  
Microporous Polymers ◽  
Exciton Migration ◽  
Wide Range ◽  
Function Relationship ◽  
Relationship Of ◽  
Conjugated Microporous Polymers

Fluorescent porous organic polymers are a unique class of materials owing to their strong aggregation induced emission, long range exciton migration and permanent porosity, thus envisioned to possess a wide range of applications (sensing, OLEDs).

scholarly journals Genome-wide integration site detection using Cas9 enriched amplification-free long-range sequencing

2020 ◽  
Author(s):  
Joost van Haasteren ◽  
Altar M Munis ◽  
Deborah R Gill ◽  
Stephen C Hyde
Keyword(s):  
Long Range ◽  
Insertional Mutagenesis ◽  
Lentiviral Vector ◽  
Integration Site ◽  
Low Cost ◽  
Safety Evaluation ◽  
Read Length ◽  
Chromosomal Dna ◽  
Wide Range

Abstract The gene and cell therapy fields are advancing rapidly, with a potential to treat and cure a wide range of diseases, and lentivirus-based gene transfer agents are the vector of choice for many investigators. Early cases of insertional mutagenesis caused by gammaretroviral vectors highlighted that integration site (IS) analysis was a major safety and quality control checkpoint for lentiviral applications. The methods established to detect lentiviral integrations using next-generation sequencing (NGS) are limited by short read length, inadvertent PCR bias, low yield, or lengthy protocols. Here, we describe a new method to sequence IS using Amplification-free Integration Site sequencing (AFIS-Seq). AFIS-Seq is based on amplification-free, Cas9-mediated enrichment of high-molecular-weight chromosomal DNA suitable for long-range Nanopore MinION sequencing. This accessible and low-cost approach generates long reads enabling IS mapping with high certainty within a single day. We demonstrate proof-of-concept by mapping IS of lentiviral vectors in a variety of cell models and report up to 1600-fold enrichment of the signal. This method can be further extended to sequencing of Cas9-mediated integration of genes and to in vivo analysis of IS. AFIS-Seq uses long-read sequencing to facilitate safety evaluation of preclinical lentiviral vector gene therapies by providing IS analysis with improved confidence.

scholarly journals Modelling H2 and its effects on star formation using a joint implementation of gadget-3 and KROME

2021 ◽  
Vol 504 (2) ◽  
pp. 2325-2345
Author(s):  
Emanuel Sillero ◽  
Patricia B Tissera ◽  
Diego G Lambas ◽  
Stefano Bovino ◽  
Dominik R Schleicher ◽  
...  
Keyword(s):  
Star Formation ◽  
Formation Rate ◽  
Physical Parameters ◽  
Density Profiles ◽  
Star Forming ◽  
Chemical Enrichment ◽  
Numerical Resolution ◽  
Stellar Radiation ◽  
Wide Range ◽  
The Impact

ABSTRACT We present p-gadget3-k, an updated version of gadget-3, that incorporates the chemistry package krome. p-gadget3-k follows the hydrodynamical and chemical evolution of cosmic structures, incorporating the chemistry and cooling of H2 and metal cooling in non-equilibrium. We performed different runs of the same ICs to assess the impact of various physical parameters and prescriptions, namely gas metallicity, molecular hydrogen formation on dust, star formation recipes including or not H2 dependence, and the effects of numerical resolution. We find that the characteristics of the simulated systems, both globally and at kpc-scales, are in good agreement with several observable properties of molecular gas in star-forming galaxies. The surface density profiles of star formation rate (SFR) and H2 are found to vary with the clumping factor and resolution. In agreement with previous results, the chemical enrichment of the gas component is found to be a key ingredient to model the formation and distribution of H2 as a function of gas density and temperature. A star formation algorithm that takes into account the H2 fraction together with a treatment for the local stellar radiation field improves the agreement with observed H2 abundances over a wide range of gas densities and with the molecular Kennicutt–Schmidt law, implying a more realistic modelling of the star formation process.

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