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  1. Article ; Online: Distance-dependent dielectric constant at the calcite/electrolyte interface: Implication for surface complexation modeling.

    Zarzycki, Piotr

    Journal of colloid and interface science

    2023  Volume 645, Page(s) 752–764

    Abstract: Hypothesis: The electrical double layer formed at the mineral/electrolyte interface is often modeled using mean-field approaches based on a continuum description of the solvent whose dielectric constant is assumed to decrease monotonically with ... ...

    Abstract Hypothesis: The electrical double layer formed at the mineral/electrolyte interface is often modeled using mean-field approaches based on a continuum description of the solvent whose dielectric constant is assumed to decrease monotonically with decreasing distance to the surface. In contrast, molecular simulations show that the solvent polarizability oscillates near the surface similar to the water density profile - as shown previously, for example, by Bonthuis et al. (D.J. Bonthuis, S. Gekle, R.R. Netz, Dielectric Profile of Interfacial Water and its Effect on Double-Layer Capacitance, Phys Rev Lett 107(16) (2011) 166102). We showed that molecular and mesoscale pictures agree by spatially averaging the dielectric constant obtained from molecular dynamics simulations over the distances relevant to the mean-field representation. In addition, the values of capacitances used to describe the electrical double layer in Surface Complexation Models (SCMs) of the mineral/electrolyte interface can be estimated using molecularly informed spatially averaged dielectric constants and positions of hydration layers.
    Experiments: First, we used molecular dynamics simulations to model the calcite 101¯4/electrolyte interface. Next, by using atomistic trajectories, we calculated the distance-dependent static dielectric constant and water density in the direction normal to the. Finally, we applied spatial compartmentalization consistent with the model of parallel-plate capacitors connected in series to estimate SCM capacitances.
    Findings: Computationally expensive simulations are required to determine the dielectric constant profile of interfacial water near the mineral surface. On the other hand, water density profiles are readily assessable from much shorter simulation trajectories. Our simulations confirmed that dielectric and water density oscillations at the interface are correlated. Here, we parametrized linear regression models to estimate the dielectric constant directly from the local water density. This is a significant computational shortcut compared to slowly converging calculations relying on total dipole moment fluctuations. The amplitude of the interfacial dielectric constant oscillation can exceed the dielectric constant of the bulk water, suggesting an ice-like frozen state, but only if there are no electrolyte ions. The interfacial accumulation of electrolyte ions causes a decrease in the dielectric constant due to the reduction of water density and re-orientation of water dipoles in ion hydration shells. Finally, we show how to use the computed dielectric properties to estimate SCM's capacitances.
    Language English
    Publishing date 2023-05-05
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241597-5
    ISSN 1095-7103 ; 0021-9797
    ISSN (online) 1095-7103
    ISSN 0021-9797
    DOI 10.1016/j.jcis.2023.04.169
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Distance-dependent dielectric constant at the calcite/electrolyte interface: Implication for surface complexation modeling

    Zarzycki, Piotr

    Journal of Colloid And Interface Science. 2023 Sept., v. 645 p.752-764

    2023  

    Abstract: The electrical double layer formed at the mineral/electrolyte interface is often modeled using mean-field approaches based on a continuum description of the solvent whose dielectric constant is assumed to decrease monotonically with decreasing distance ... ...

    Abstract The electrical double layer formed at the mineral/electrolyte interface is often modeled using mean-field approaches based on a continuum description of the solvent whose dielectric constant is assumed to decrease monotonically with decreasing distance to the surface. In contrast, molecular simulations show that the solvent polarizability oscillates near the surface similar to the water density profile – as shown previously, for example, by Bonthuis et al. (D.J. Bonthuis, S. Gekle, R.R. Netz, Dielectric Profile of Interfacial Water and its Effect on Double-Layer Capacitance, Phys Rev Lett 107(16) (2011) 166102). We showed that molecular and mesoscale pictures agree by spatially averaging the dielectric constant obtained from molecular dynamics simulations over the distances relevant to the mean-field representation. In addition, the values of capacitances used to describe the electrical double layer in Surface Complexation Models (SCMs) of the mineral/electrolyte interface can be estimated using molecularly informed spatially averaged dielectric constants and positions of hydration layers. First, we used molecular dynamics simulations to model the calcite 101¯4/electrolyte interface. Next, by using atomistic trajectories, we calculated the distance-dependent static dielectric constant and water density in the direction normal to the. Finally, we applied spatial compartmentalization consistent with the model of parallel-plate capacitors connected in series to estimate SCM capacitances. Computationally expensive simulations are required to determine the dielectric constant profile of interfacial water near the mineral surface. On the other hand, water density profiles are readily assessable from much shorter simulation trajectories. Our simulations confirmed that dielectric and water density oscillations at the interface are correlated. Here, we parametrized linear regression models to estimate the dielectric constant directly from the local water density. This is a significant computational shortcut compared to slowly converging calculations relying on total dipole moment fluctuations. The amplitude of the interfacial dielectric constant oscillation can exceed the dielectric constant of the bulk water, suggesting an ice-like frozen state, but only if there are no electrolyte ions. The interfacial accumulation of electrolyte ions causes a decrease in the dielectric constant due to the reduction of water density and re-orientation of water dipoles in ion hydration shells. Finally, we show how to use the computed dielectric properties to estimate SCM's capacitances.
    Keywords calcite ; capacitance ; dielectric properties ; electrolytes ; models ; molecular dynamics ; regression analysis ; solvents ; Interfacial dielectric constant ; Electric double layer ; Ice-like water ; Calcite/electrolyte interface
    Language English
    Dates of publication 2023-09
    Size p. 752-764.
    Publishing place Elsevier Inc.
    Document type Article ; Online
    ZDB-ID 241597-5
    ISSN 1095-7103 ; 0021-9797
    ISSN (online) 1095-7103
    ISSN 0021-9797
    DOI 10.1016/j.jcis.2023.04.169
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Machine learning surrogates for surface complexation model of uranium sorption to oxides.

    Li, Chunhui / Adeniyi, Elijah O / Zarzycki, Piotr

    Scientific reports

    2024  Volume 14, Issue 1, Page(s) 6603

    Abstract: The safety assessments of the geological storage of spent nuclear fuel require understanding the underground radionuclide mobility in case of a leakage from multi-barrier canisters. Uranium, the most common radionuclide in non-reprocessed spent nuclear ... ...

    Abstract The safety assessments of the geological storage of spent nuclear fuel require understanding the underground radionuclide mobility in case of a leakage from multi-barrier canisters. Uranium, the most common radionuclide in non-reprocessed spent nuclear fuels, is immobile in reduced form (U(IV) and highly mobile in an oxidized state (U(VI)). The latter form is considered one of the most dangerous environmental threats in the safety assessments of spent nuclear fuel repositories. The sorption of uranium to mineral surfaces surrounding the repository limits their mobility. We quantify uranium sorption using surface complexation models (SCMs). Unfortunately, numerical SCM solvers often encounter convergence problems due to the complex nature of convoluted equations and correlations between model parameters. This study explored two machine learning surrogates for the 2-pK Triple Layer Model of uranium retention by oxide surfaces if released as U(IV) in the oxidizing conditions: random forest regressor and deep neural networks. Our surrogate models, particularly DNN, accurately reproduce SCM model predictions at a fraction of the computational cost without any convergence issues. The safety assessment of spent fuel repositories, specifically the migration of leaked radioactive waste, will benefit from having ultrafast AI/ML surrogates for the computationally expensive sorption models that can be easily incorporated into larger-scale contaminant migration models. One such model is presented here.
    Language English
    Publishing date 2024-03-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-024-57026-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning.

    Li, Chunhui / Gilbert, Benjamin / Farrell, Steven / Zarzycki, Piotr

    Journal of chemical information and modeling

    2023  Volume 63, Issue 12, Page(s) 3742–3750

    Abstract: Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages over ... ...

    Abstract Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages over visited molecular configurations - microstates. However, to obtain convergence, we need a sufficiently long record of visited microstates, which translates to the high-computational cost of the molecular simulations. In this work, we show how to use a point cloud-based deep learning strategy to rapidly predict the structural properties of liquids from a single molecular configuration. We tested our approach using three homogeneous liquids with progressively more complex entities and interactions: Ar, NO, and H
    MeSH term(s) Deep Learning ; Molecular Dynamics Simulation ; Molecular Conformation ; Temperature ; Neural Networks, Computer
    Language English
    Publishing date 2023-06-12
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.3c00472
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: The Steady March toward Biomimetic Nanoelectronics.

    Rosso, Kevin M / Zarzycki, Piotr

    ACS nano

    2021  Volume 15, Issue 5, Page(s) 7844–7847

    Abstract: Steady progress is being made in unveiling nature's long-range charge transport mechanisms in redox proteins and in the development of versatile self-assembling scaffolds ... ...

    Abstract Steady progress is being made in unveiling nature's long-range charge transport mechanisms in redox proteins and in the development of versatile self-assembling scaffolds and
    MeSH term(s) Bacteria/metabolism ; Biomimetics ; Electron Transport ; Heme/metabolism ; Oxidation-Reduction
    Chemical Substances Heme (42VZT0U6YR)
    Language English
    Publishing date 2021-05-17
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 1936-086X
    ISSN (online) 1936-086X
    DOI 10.1021/acsnano.1c01923
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Effect of the Addition of Low-Alkaloid Lupine Flour on the Glycemic Index In Vivo and the Physicochemical Properties and Cooking Quality of Durum Wheat Pasta.

    Krawęcka, Ada / Sobota, Aldona / Zarzycki, Piotr

    Foods (Basel, Switzerland)

    2022  Volume 11, Issue 20

    Abstract: The aim of this research was to determine the effect of the addition of lupine flour (LF) on the values of the glycemic index (GI) and glycemic load (GL), physicochemical properties, and cooking quality of durum semolina pasta. The pasta was enriched ... ...

    Abstract The aim of this research was to determine the effect of the addition of lupine flour (LF) on the values of the glycemic index (GI) and glycemic load (GL), physicochemical properties, and cooking quality of durum semolina pasta. The pasta was enriched with 0-25% of lupine flour (LF0-LF25). Additionally, 7.5 and 20% of oat β-glucans, 5% of vital gluten, and 20% of millet flour were used in a selected sample. The addition of 7.5% β-glucans and 5% vital gluten to the product resulted in only a slight decrease in the GI of the products. A significant decrease in pasta GI was noted after the addition of 20% of lupine flour. The product enriched with 20% of lupine flour, 20% of β-glucans, and 20% of millet flour had the lowest glycemic index and glycemic load (GI = 33.75%, GL = 7.2%, respectively). At the same time, the lupine-flour-enriched products were characterized by an increased concentration of protein, fat, ash, and dietary fiber. The addition of lupine flour at the level of up to 20% yielded functional products characterized by good cooking quality.
    Language English
    Publishing date 2022-10-14
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704223-6
    ISSN 2304-8158
    ISSN 2304-8158
    DOI 10.3390/foods11203216
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Interfacial water screens the protein-induced transmembrane voltage.

    Zarzycki, Piotr

    The journal of physical chemistry. B

    2015  Volume 119, Issue 4, Page(s) 1474–1482

    Abstract: Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays ...

    Abstract Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays a special role. Water structural ordering generates the dipole potential that typically overcompensates for an intrinsic membrane-protein potential gradient, and thus it modifies and sustains an overall cellular electrostatics. Although the transmembrane voltage has been extensively studied, the dipole potential has attracted very little attention. Here, by using molecular dynamics, we examined water electrostatic response to the transmembrane charge, field, and potential asymmetry introduced by the presence of four integral membrane proteins: typical of inner (α-helix) and outer membrane (β-barrel). In all cases, the protein presence introduces electrostatic directionality in the transmembrane dipole field and voltage. In particular, water generates a deep potential sink if strongly polar residues are densely packed on one side of bilayer, as frequently occurs in a selectivity filter of the K(+) channel. We also found that protein secondary structure is less important than the polar residue distribution along the protein channel. Our findings are relevant for understanding the driving force behind biomembrane conductivity: the ability of biological water to electrostatically screen the transmembrane voltage.
    MeSH term(s) Escherichia coli Proteins/chemistry ; Membrane Potentials ; Membrane Proteins/chemistry ; Models, Molecular ; Water/chemistry
    Chemical Substances Escherichia coli Proteins ; Membrane Proteins ; Water (059QF0KO0R)
    Language English
    Publishing date 2015-01-29
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/jp509329u
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Temperature-dependence of the dielectric relaxation of water using non-polarizable water models.

    Zarzycki, Piotr / Gilbert, Benjamin

    Physical chemistry chemical physics : PCCP

    2019  Volume 22, Issue 3, Page(s) 1011–1018

    Abstract: Key physical and chemical properties of aqueous fluids are determined by the structure and dynamics of the hydrogen bond network of water but we lack adequate models for the linkages between hydrogen bonding and aqueous chemistry, particularly in non- ... ...

    Abstract Key physical and chemical properties of aqueous fluids are determined by the structure and dynamics of the hydrogen bond network of water but we lack adequate models for the linkages between hydrogen bonding and aqueous chemistry, particularly in non-ambient conditions or in confinement. Dielectric relaxation spectroscopy (DRS) provides a sensitive approach for probing water dynamics but sound interpretation of DRS data requires molecular simulation and associated computational methods capable of accurately representing aqueous fluids and their frequency dependent, complex permittivity. Here, we test the accuracy of dielectric spectra of bulk liquid water calculated from molecular dynamics simulations using 19 non-polarizable water models at 298 K. In contrast to prior studies, the simulation size, time-step and duration allow calculation of the dielectric function from 107-1012 Hz without assuming an analytical form. The accuracy of the prediction of the low-frequency (static) dielectric constant at room temperature is related to the water molecule dipole moment, specifically models with μ ≥ 2.4 D give ε(0) with a relative error lower than 5%. However, no water model tested can fully reproduce the complex dielectric spectra of water. For a subset of models, calculations of the dielectric response from -5 to 60 °C reproduces the experimental trend in water dynamics with temperature but the characteristic relaxation time is always underestimated. The calculated water dipole relaxation time and hydrogen-bond lifetime are both exponentially decaying functions of temperature, and exhibit a linear correlation very close to equality. The comparison provides new computational support for the concept that the Debye relaxation of liquid water is determined by the dynamics of the hydrogen-bond network, and that both are ensemble properties.
    Language English
    Publishing date 2019-12-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c9cp04578c
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Interfacial Water Screens the Protein-Induced Transmembrane Voltage

    Zarzycki, Piotr

    Journal of physical chemistry. 2015 Jan. 29, v. 119, no. 4

    2015  

    Abstract: Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays ...

    Abstract Transmembrane proteins are crucial in cellular traffic, signal transduction, and energy storage in a form of transmembrane voltage. These proteins are stabilized by hydrophobic and hydrophilic interactions, in which cytoplasmic and exoplasmic water plays a special role. Water structural ordering generates the dipole potential that typically overcompensates for an intrinsic membrane–protein potential gradient, and thus it modifies and sustains an overall cellular electrostatics. Although the transmembrane voltage has been extensively studied, the dipole potential has attracted very little attention. Here, by using molecular dynamics, we examined water electrostatic response to the transmembrane charge, field, and potential asymmetry introduced by the presence of four integral membrane proteins: typical of inner (α-helix) and outer membrane (β-barrel). In all cases, the protein presence introduces electrostatic directionality in the transmembrane dipole field and voltage. In particular, water generates a deep potential sink if strongly polar residues are densely packed on one side of bilayer, as frequently occurs in a selectivity filter of the K⁺ channel. We also found that protein secondary structure is less important than the polar residue distribution along the protein channel. Our findings are relevant for understanding the driving force behind biomembrane conductivity: the ability of biological water to electrostatically screen the transmembrane voltage.
    Keywords asymmetry ; cell membranes ; energy ; hydrophilic interactions ; hydrophobicity ; molecular dynamics ; physiological transport ; potassium channels ; protein secondary structure ; signal transduction ; transmembrane proteins
    Language English
    Dates of publication 2015-0129
    Size p. 1474-1482.
    Publishing place American Chemical Society
    Document type Article
    ISSN 1520-5207
    DOI 10.1021%2Fjp509329u
    Database NAL-Catalogue (AGRICOLA)

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  10. Article: Effect of Moldavian dragonhead seed residue on the baking properties of wheat flour and bread quality

    Zarzycki, Piotr / Wirkijowska, Anna / Nawrocka, Agnieszka / Kozłowicz, Katarzyna / Krajewska, Marta / Kłosok, Konrad / Krawęcka, Ada

    Lebensmittel-Wissenschaft + [i.e. und] Technologie. 2022 Feb. 01, v. 155

    2022  

    Abstract: The effect of adding defatted Moldavian dragonhead seed residue flour (MDF) at concentrations of 3–12% (w/w flour basis) to wheat flour on dough rheology and bread quality was investigated in the present study. The farinograph characteristics show that ... ...

    Abstract The effect of adding defatted Moldavian dragonhead seed residue flour (MDF) at concentrations of 3–12% (w/w flour basis) to wheat flour on dough rheology and bread quality was investigated in the present study. The farinograph characteristics show that supplementation of the wheat flour dough with MDF increases water absorption and dough softening but decreases the stability time. Regarding the effect on bread properties, the addition of MDF increased the bread yield and decreased baking loss, porosity, taste, and bread volume compared to the control (100% wheat flour). In addition, the partial replacement of wheat flour with MDF had a significant effect (p ≤ 0.05) on hardness and chewiness; both these textural indices were increased. A significant reduction in lightness (L*) and yellowness (b*) and an increase in redness (a*) induced by the MDF addition were observed in the bread crumb. Therefore, MDF at the concentration up to 6 g/100 g can be used to produce bread with good consumer acceptance. We found that the 6 g/100 g MDF addition to the bread formula provided an increase of 59% in dietary fiber, 32% in fat, and 50% in minerals, with significantly lower carbohydrate content and energy value compared to the control.
    Keywords breadmaking quality ; breads ; carbohydrate content ; chewiness ; consumer acceptance ; dietary fiber ; dough ; energy ; hardness ; porosity ; rheology ; taste ; water uptake ; wheat flour
    Language English
    Dates of publication 2022-0201
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 241369-3
    ISSN 0460-1173 ; 0023-6438
    ISSN 0460-1173 ; 0023-6438
    DOI 10.1016/j.lwt.2021.112967
    Database NAL-Catalogue (AGRICOLA)

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