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Texto publicado originalmente em 28 de março de 2022 na The Stanford Encyclopedia of Philosophy . A tradução segue a versão nos arquivos do SEP, disponível em: . Esta versão traduzida, portanto, pode diferir da versão final, que pode ter sido atualizada desde o momento desta tradução. A versão atual está disponível em: e . Gostaríamos de agradecer ao autor e editores da Stanford Encyclopedia of Philosophy por conceder permissão para traduzir e publicar este verbete na REVER. O tradutor optou por manter a formatação original do verbete, estando fora das normas típicas de submissão da REVER.

Carbon-based nanosheet membranes with functionalized pores have great potential as water treatment membranes. In this study, the separation of Hg2+ and Cu2+ as heavy metal ions from aqueous solutions using a functionalized γ-graphyne-1 nanosheet membrane is investigated by molecular dynamics simulations. The simulation systems consist of a γ-graphyne-1 nanosheet with −COOH or −NH2 functional groups on the edge of pores placed in an aqueous solution containing CuCl2 and HgCl2. An external electric field is applied as a driving force across the membrane for the separation of heavy metal ions using these functionalized pores. The ion–membrane and water molecule–membrane interaction energies, the radial distribution function of cations, the retention time and permeation of ions through the membrane, the density profile of water and ions, and the hydrogen bond in the system are investigated, and these results reveal that the performance of −NH2-functionalized γ-graphyne-1 is better than that of −COOH-functionalized γ-graphyne-1 in the separation of Cu2+, while the Hg2+ cations encounter a high energy barrier as they pass through the membrane, especially in the −COOH-functionalized pore, due to their larger ionic radius and the smaller pore size of this membrane.

“Historicity” describes the human condition during one’s life course, marked by contingency and freedom, temporality and finitude. The concept also occurs in evolutionary biology, social sciences a...

Hydrodynamic flow in the spider duct induces conformational changes in dragline spider silk proteins (spidroins) and drives their assembly, but the underlying physical mechanisms are still elusive. Here we address this challenging multiscale problem with a complementary strategy of atomistic and coarse-grained Molecular Dynamics (MD) simulations with uniform flow. The conformational changes at the molecular level were analyzed for single tethered spider silk peptides. Uniform flow leads to coiled-to-stretch transitions and pushes alanine residues intoβ-sheet and Poly-Proline II (PPII) conformations. Coarse-grained simulations of the assembly process of multiple semi-flexible block copolymers using multi-particle collision dynamics reveal that the spidroins aggregate faster but into low-order assemblies when they are less extended. At medium-to-large peptide extensions (50%-80%), assembly slows down and becomes reversible with frequent association and dissociation events, while spidroin alignment increases and alanine repeats form ordered regions. Our work highlights the role of flow in guiding silk self-assembly into tough fibers by enhancing alignment and kinetic reversibility, a mechanism likely relevant for other proteins whose function depends on hydrodynamic flow.

Two-dimensional nanoporous carbon-based membrane has proved to be a promising reverse osmosis (RO) membrane for contaminated ions separation from water. In this study, molecular dynamics simulations are conducted to assess the performance of C2N and g-C3N4 nanosheets for the separation of nitrate and nitrite pollutants from aqueous solution. The nitrate and nitrite rejection were obtained 100 % for both membranes at high pressures, with water fluxes of 25.38 L/cm2DayMPa and 9.13 L/cm2DayMPa through C2N and g-C3N4 membranes, respectively. We observed that the water self-diffusivity increased 3 times in the presence of the C2N and g-C3N4 nonporous membrane, due to the hydrophilic structure of these membranes. The results of potential of the mean force (PMF) for nitrate and nitrite ions confirm the high ions rejection capability of these membranes at high pressure, where hydrogen bonding dynamics enhances water flux.

Using molecular dynamic simulations, the performance of carbon nitride (C2N) was studied for the separation of Cu2+ and Hg2+ as heavy metal ions from water. The high porosity of the single layer C2N nanosheet in comparison with other similar carbon-based membranes and the existence of nitrogen atoms at the edge of the pores increase the efficiency of C2N for water purification. The separation of heavy metal ions through the nanosheet is performed by applying an external voltage across the membrane. Investigation of the ions permeation through the membrane demonstrates that the permeability of the Cu2+ ions through the C2N is about 2.5 times higher than that of Hg2+. The results of radial pair distribution function analysis illustrate that the energy barrier for ions passage is due to the hydration shell of the cations. Also, the density of the cations and water molecules, and the hydrogen bonds between water molecules in the whole system are analysed for the study of the performance of C2N nanosheet for ion separation and these results demonstrate that this membrane has the selectivity performance for heavy metal removal and higher permeability of the cations than that of other carbon-based membrane because of high porosity.

A molecular dynamics simulation study is conducted to investigate the capability of the pristine graphdiyne nanosheet for nitrate ion separation from water. The removal of nitrate ion contaminants from water is of critical importance as it represents an environmental hazard. The graphdiyne is a carbon-based membrane with pore density of 2.4 × 1018 pores/m2 and incircle radius of 2.8 Å. We show that the efficient water flow is accurately controlled through fine regulation of the exerted hydrostatic pressure. The high water permeability of 6.19 L.Day−1cm−2MPa−1 with 100% nitrate ions rejection suggests that the graphdiyne can perform as a suitable membrane for nitrate separation. The potential of mean force analysis of the single water molecule and nitrate ion indicated the free energy barriers for nitrate of about 4 times higher than that of water molecules. The results reveal the weak interaction of the water molecules and the membrane which aid to high water flux.

Nearly frictionless water transport makes carbon nanotubes promising materials for use as conduits in nanofluidic applications. Here, we conduct molecular dynamics simulations of water flow within amorphous silica nanopores coated by a (39,39) single-walled carbon nanotube (SWCNT). Our atomistic models describe the interaction between water and pore walls based on two possible scenarios, translucency and opacity to wetting of a SWCNT. Simulation results indicate that the SWCNT coating enhances water flow through silica pores ca. 10 times compared to predictions from the classical Hagen–Poiseuille relation. By varying the strength of the water–pore interaction, we study the relationship between surface wettability and hydrodynamic slippage. We observe an increase in the slip length for higher values of water contact angle. Moreover, cases with SWCNT opacity and translucency to wetting display a substantial difference in the computed slippage, showing that the water contact angle is not the only factor that determines the slip boundary condition under nanoconfinement. We attribute this disparity to the corrugation of the potential energy landscape at the inner pore wall. The present study provides a theoretical framework for the use of carbon nanotube-based coatings in designing more efficient nanofluidic conduits.

Nanocomposites built from polymers and carbon nanotubes (CNTs) are a promising class of materials. Computer modeling can provide nanoscale views of the polymer–CNT interface, which are much needed to foster the manufacturing and development of such materials. However, setting up periodic nanocomposite models is a challenging task. Here we propose a computational workflow based on Molecular Dynamics simulations. We demonstrate its capabilities and showcase its applications, focusing on two existing nanocomposite materials: polystyrene (PS) with CNT and polyether ether ketone with CNT. The models provide insights into the polymer crystallization inside CNTs. Furthermore, the PS+CNT nanocomposite models are mechanically tested and able to predict an enhancement in Young’s modulus due to the addition of highly dispersed CNTs. We accompany those results with experimental tests and provide a prediction model based on Dynamic Quantized Fracture Mechanics theory. Our study proposes representative simulations of polymer–CNT nanocomposites as promising tools to guide the rational design of this class of materials.

Engineering at nanoscale holds the promise of tuning materials with extraordinary properties. However, macroscopic approaches commonly used to predict mechanical properties do not fully apply at nanoscale level. A controversial feature is the presence of nanoflaws in aragonite nacre, as it is expected that flaws would weaken the material, whereas nacre still shows high toughness and rupture strength. Here, we performed molecular dynamics and finite element simulations emulating flaws found in aragonite nacre. Our simulations reveal two regimes for fracture: nacre remains flaw-insensitive only for flaws smaller than 1.2 nm depth, or flaws of a few atoms, whereas larger flaws follow a Griffith-like trend resembling macroscopic fracture. We tested an alternative mechanism for flaw-insensitivity in nacre, and investigated the mechanical effect of organic filling to mitigate fracture. We found that a single nacre protein, perlucin, decreases the stress concentration at the fracture point, producing enhancements of up to 15% in rupture strength. Our study reveals a more comprehensive understanding of mechanical stability at the nanoscale and offers new routes toward hybrid nanomaterials.

In this work, a novel comparative method for highly brittle materials such as aragonite crystals is proposed, which provides an efficient and accurate in-sight understanding for multi-scale fracture modeling. In particular, physically-motivated molecular dynamics (MD) simulations are performed to model quasi-static brittle crack propagation on the nano-scale and followingly compared to macroscopic modeling of fracture using the phase-field modeling (PFM) technique. A link between the two modeling schemes is later proposed by deriving PFM parameters from the MD atomistic simulations. Thus, in this combined approach, MD simulations provide a more realistic meaning and physical estimation of the PFM parameters. The proposed computational approach, that encompasses mechanics on discrete and continuum levels, can assist multi-scale modeling and easing, for instance, the simulation of biological materials and the design of new materials.

Some transhumanists argue that we must engage with theories and facts about our evolutionary past in order to promote future enhancements of the human body. At the same time, they call our attention to the flawed character of evolution and argue that there is a mismatch between adaptation to ancestral environments and contemporary life. One important trait of our evolutionary past which should not be ignored, and yet may hinder the continued perfection of humankind, is the peculiarly human way of bearing and raising children. The suffering associated with childbirth and a long childhood have demanded trade-offs that have enhanced our species, leading to cooperation, creativity, intelligence and resilience. Behaviors such as mother–infant engagement, empathy, storytelling, and ritual have also helped to create what we value most in human beings. Therefore, the moral, cognitive, and emotional enhancements proposed by these transhumanists may be impaired by their partial appropriation of evolution, insofar as the bittersweet experience of parenthood is left aside.

Transhumanist thought on overpopulation usually invokes the welfare of present human beings and the control over future generation, thus minimizing the need and meaning of new births. Here we devise a framework for a more thorough screening of the relevant literature, to have a better appreciation of the issue of natality. We follow the lead of Hannah Arendt and Brent Waters in this respect. With three overlapping categories of words, headed by “natality,” “birth,” and “intergenerations,” a large sample of books on transhumanism is scrutinized, showing the lack of sustained reflection on the issue. After this preliminary scrutiny, a possible defense of natality in face of modern and transhumanist thought is marshaled, evoking a number of desirable human traits. One specific issue, the impact of modern values on natality, is further explored, reiterating that concerns about overpopulation and enhanced humans should keep in sight the natural cycle of birth and death.

How far has theology departed from both religion and science, insofar as it intends to be accountable to the Academy? Our argument shows that insights on this issue can be drawn from the current discussion in the cognitive science of religion (CSR). Robert McCauley's arguments on this matter, represented by the image of “Lot's Wife's temptation,” are discussed here around four topics: the unnaturalness of religion, the naturalness of science, the scientificity of Biblical scholarship, as well as (partially) of theology. This discussion engages three of McCauley's publications, which are analyzed with the purpose of assessing the appropriateness of this image. It is shown that, despite many insights that it may provide, neither science nor theology are adequately represented in the image of “Lot's Wife.”

Nanopores in thin synthetic membranes have emerged as convenient tools for high-throughput single-molecule manipulation and analysis. Because of their small sizes and their ability to selectively transport solutes through otherwise impermeable membranes, nanopores have numerous potential applications in nanobiotechnology. For most applications, properties of the nanopore systems have to be characterize at the atomic level, which is currently beyond the limit of experimental methods. Molecular dynamics (MD) simulations can provide the desired information, however several technical challenges have to be met before this method can be applied to synthetic nanopore systems. Here, we highlight our recent work on modeling synthetic nanopores of the most common types. First, we describe a novel graphical tool for setting up all-atom systems incorporating inorganic materials and biomolecules. Next, we illustrate the application of the MD method for silica, silicon nitride, and polyethylene terephthalate nanopores. Following that, we describe a method for modeling synthetic surfaces using a bias potential. Future directions for tool development and nanopore modeling are briefly discussed at the end of this article.

Amorphous silica is an inorganic material that is central for many nanotechnology appplications, such as nanoelectronics, microfluidics, and nanopore sensors. To use molecular dynamics (MD) simulations to study the behavior of biomolecules interacting with silica, we developed a force field for amorphous silica surfaces based on their macroscopic wetting properties that is compatible with the CHARMM force field and TIP3P water model. The contact angle of a water droplet on a silica surface served as a criterion to tune the intermolecular interactions. The resulting force field was used to study the permeation of water through silica nanopores, illustrating the influence of the surface topography and the intermolecular parameters on permeation kinetics. We find that minute modeling of the amorphous surface is critical for MD studies, since the particular arrangement of surface atoms controls sensitively electrostatic interactions between silica and water.

Spider dragline silk, solely made from protein, outperforms synthetic fibers in terms of toughness and extensibility, which is thought to originate from its refined nano-scale hierarchical structure. The key for understanding the outstanding mechanical performance of dragline silk lies in a detailed description of the underlying molecular structure and dynamics under load conditions. Here, we aim at determining the ingredients for silk's outstanding toughness using multi-scale computational simulations. First, we present large-scale molecular-dynamics simulations of the structure and dynamics of silk protein. We introduce the most comprehensive, to date, spider silk models comprising of hundred 500-residue chains of two spider proteins, namely MaSp1 and MaSp2, using a collapsing-annealing protocol [1]. Our systems are composed of crystalline beta-sheet segments completely embedded in and connected with an amorphous phase. On this basis, we developed a three-dimensional continuum model of dragline silk for finite element analysis. Such model takes into account the plasticity of the beta-sheets, the rate-dependent dynamics of the amorphous phase, and the viscous friction between them [2]. Tensile properties, velocity-dependent effects and hysteresis are in good agreement with experimental data. Intriguingly, the simulations revealed that under load conditions, crystals rearrange into lamellar bands. We could confirm this trend by small-angle neutron scattering of silk fibers under stress, with simulations and experiments showing quantitatively the same shift and intensity in the signal from the periodically forming bands. The increased order results in a more homogenous stress distribution and higher fiber toughness. Our combined atomistic and fiber-level simulations and experiments suggest that the test stress-induced order is a common feature in materials combining crystalline and amorphous phases on the nano-scale.[1] Cruz-Chu, E. R et al. Faraday Discussions (2009) 143, 47-62[2] Sandeep Patil et al. PLOS One (2014) 9, e104832

Rough surfaces immersed under water remain practically dry if the liquid-solid contact is on roughness peaks, while the roughness valleys are filled with gas. Mechanisms that prevent water from invading the valleys are well studied. However, to remain practically dry under water, additional mechanisms need consideration. This is because trapped gas (e.g. air) in the roughness valleys can dissolve into the water pool, leading to invasion. Additionally, water vapor can also occupy the roughness valleys of immersed surfaces. If water vapor condenses, that too leads to invasion. These effects have not been investigated, and are critically important to maintain surfaces dry under water. In this work, we identify the critical roughness scale, below which it is possible to sustain the vapor phase of water and/or trapped gases in roughness valleys – thus keeping the immersed surface dry. Theoretical predictions are consistent with molecular dynamics simulations and experiments., Scientific Reports, 5, ISSN:2045-2322

The glycocalyx is a sugar-rich layer located at the luminal part of the endothelial cells. It is involved in key metabolic processes and its malfunction is related to several diseases. To understand the function of the glycocalyx, a molecular level characterization is necessary. In this article, we present large-scale molecular-dynamics simulations that provide a comprehensive description of the structure and dynamics of the glycocalyx. We introduce the most detailed, to-date, all-atom glycocalyx model, composed of lipid bilayer, proteoglycan dimers, and heparan sulfate chains with realistic sequences. Our results reveal the folding of proteoglycan ectodomain and the extended conformation of heparan sulfate chains. Furthermore, we study the glycocalyx response under shear flow and its role as a flypaper for binding fibroblast growth factors (FGFs), which are involved in diverse functions related to cellular differentiation, including angiogenesis, morphogenesis, and wound healing. The simulations show that the glycocalyx increases the effective concentration of FGFs, leading to FGF oligomerization, and acts as a lever to transfer mechanical stimulus into the cytoplasmic side of endothelial cells.

Carbon nanotube (CNT) membranes hold the promise of extraordinary fast water transport for applications such as energy efficient filtration and molecular level drug delivery. However, experiments and computations have reported flow rate enhancements over continuum hydrodynamics that contradict each other by orders of magnitude. We perform large scale molecular dynamics simulations emulating for the first time the micrometer thick CNTs membranes used in experiments. We find transport enhancement rates that are length dependent due to entrance and exit losses but asymptote to 2 orders of magnitude over the continuum predictions. These rates are far below those reported experimentally. The results suggest that the reported superfast water transport rates cannot be attributed to interactions of water with pristine CNTs alone.

“North-South” divides usually overlook the fact that Latin America was also part of the New World. It was only after WW II that these countries were lumped together in a large bunch called “third world.” For the sake of simplicity, this paper restricts itself to the period when Liberation Theology made its appearance until now. Even though the seventies devised an autonomous Christianity, with its own traits and purposes, nowadays the churches are back in the mainstream. Issues that engage Christians there are not unlike their counterparts in “the North,” thanks to globalization. Demographic changes are still more important than cultural ones, and economic prospects are more likely to interfere in the shape of Christianity than the will and emotions of leaders and the faithful alike.

Ralph Burhoe developed his proposals for a social reformation at a time when the “two cultures” debate was still active. It is suggested here that Burhoe, sharing with his contemporaries an understanding of culture that was Western and normative in character, overlooked the distinction between the culture of the elites and popular culture, and consequently between religion as presented by theologians and church officials and popular religion. Therefore, his proposals for the revitalization of traditional religions, even if implemented, would not work. Some contradictions within his own program are pointed out, and the social role of the sciences after World War II, as well as the ambiguities of their presence in the so-called underdeveloped nations, is analyzed. As a positive conclusion, it is suggested that Burhoe's main contribution should be sought, not in his outline for a social reformation, but in his role as an organizer of the dialogue between religion and science.

Surface immobilized biomolecular probes are used in many areas of biomedical research, such as genomics, proteomics, immunology, and pathology. Although the structural conformations of small DNA and peptide molecules in free solution are well studied both theoretically and experimentally, the conformation of small biomolecules bound on surfaces, especially under the influence of external electric fields, is poorly understood. Using a combination of molecular dynamics simulation and surface-enhanced Raman spectroscopy, we study the external electric field-induced conformational change of dodecapeptide probes tethered to a nanostructured metallic surface. Surface-tethered peptides with and without phosphorylated tyrosine residues are compared to show that peptide conformational change under electric field is sensitive to biochemical modification. Our study proposes a highly sensitive in vitro nanoscale electro-optical detection and manipulation method for biomolecule conformation and charge at bio-nano interfaces.

A novel phenomenon has recently been reported in polymeric nanopores. This phenomenon, so-called nanoprecipitation, is characterized by the transient formation of precipitates in the nanopore lumen, producing a sequence of low and high conductance states in the ionic current through the pore. By means of all-atom molecular dynamics simulations, we studied nanoprecipitation for polyethylene terephthalate nanopore immersed in electrolytic solution containing calcium phosphate, covering a total simulation time of 1.24 microseconds. Our results suggest that protonable surface residues at the nanopore surface, namely carboxyl groups, trigger the formation of precipitates which strongly adhere to the surface, blocking the pore and producing the low conductance state. Based on the simulations, we propose a mechanism for the formation of the high conductance state; the mechanism involves detachment of the precipitate from the surface due to reprotonation of carboxyl groups and subsequent translocation of the precipitate out of the pore.

Computational modeling can be a useful partner in biotechnology, in particular, in nanodevice engineering. Such modeling guides development through nanoscale views of biomolecules and devices not available through experimental imaging methods. We illustrate the role of computational modeling, mainly of molecular dynamics, through four case studies: development of silicon bionanodevices for single molecule electrical recording, development of carbon nano-tube-biomolecular systems as in vivo sensors, development of lipoprotein nanodiscs for assays of single membrane proteins, and engineering of oxygen tolerance into the enzyme hydrogenase for photosynthetic hydrogen gas production. The four case studies show how molecular dynamics approaches were adapted to the specific technical uses through (i) multi-scale extensions, (ii) fast quantum chemical force field evaluation, (iii) coarse graining, and (iv) novel sampling methods. The adapted molecular dynamics simulations provided key information on device behavior and revealed development opportunities, arguing that the "computational microscope" is an indispensable nanoengineering tool.

Disordered proteins have the capacity to self-assemble from random coils to partial or complete folded structures. Such combination of amorphous/ordered phases within the protein structure is determined by the aminoacid sequence as well as enviromental factors, such as flow or confinement, and it is expected that the proportion of each phase would play a role in the activity and biological function of the protein. Nevertheless, modeling the molecular arrangement of disordered/folded structures poses a challenge and it has been possible only for few short fragments or individual proteins. For macromolecular complexes, computationally analyzing properties such as dynamics, mechanics or heat transfer requires taking the polymeric nature of chain entanglements into account. We devised a new approach based on an existing collapsing-annealing Molecular Dynamics protocol [1] for building amorphous phases of long disordered protein chains. We adapted it to also include structured phases such as beta-sheet units, by steering parts of the protein chains into the experimentally known conformations. As a proof-of-concept, we successfully set up a model of 100 intrinsically disordered chains each comprising 500 aminoacids of silk spidroin. This resulted in a compact protein-only system (20 nm)ˆ3 in size. Then, we introduced silk crystalline units based on x-ray scattering data, highlighting that our newly-develop protocol can handle composite materials with partial structure as well. Our full detail atomistic structure is the most comprehensive silk model computationally studied to date, up to our knowledge. We believe our approach to be valuable for a wide range of Molecular Dynamics simulations, in which the disordered polymeric component of proteins dominates in the assembly or biomaterial.[1] Cruz-Chu, E. R et al. Faraday Discussions (2009) 143, 47-62.

Molecular modeling is advocated here as a key methodology for research and development in bionanotechnology. Molecular modeling provides nanoscale images at atomic and even electronic resolution, predicts the nanoscale interaction of unfamiliar combinations of biological and inorganic materials, and evaluates strategies for redesigning biopolymers for nanotechnological uses. The methodology is illustrated in this paper through reviewing three case studies. The first one involves the use of single-walled carbon nanotubes as biomedical sensors where a computationally efficient, yet accurate, description of the influence of biomolecules on nanotube electronic properties through nanotube–biomolecule interactions was developed; this development furnishes the ability to test nanotube electronic properties in realistic biological environments. The second case study involves the use of nanopores manufactured into electronic nanodevices based on silicon compounds for single molecule electrical recording, in particular, for DNA sequencing. Here, modeling combining classical molecular dynamics, material science and device physics, described the interaction of biopolymers, e.g., DNA, with silicon nitrate and silicon oxide pores, furnished accurate dynamic images of pore translocation processes, and predicted signals. The third case study involves the development of nanoscale lipid bilayers for the study of embedded membrane proteins and cholesterol. Molecular modeling tested scaffold proteins, redesigned apolipoproteins found in mammalian plasma that hold the discoidal membranes in the proper shape, and predicted the assembly as well as final structure of the nanodiscs. In entirely new technological areas such as bionanotechnology, qualitative concepts, pictures and suggestions are sorely needed; these three case studies document that molecular modeling can serve a critical role in this respect, even though it may still fall short on quantitative precision.

An analysis of the backbone dynamics of the C-terminal Src homology 3 (SH3) domain of p67(phox), p67(phox)SH3(C), in complex with a 32-residue high-affinity (K(d) = 24 nM) peptide, Pf, from the C-terminal region of p47(phox) is presented. This paper represents the first detailed analysis of the backbone dynamics and the ligand-induced changes therein of a high-affinity, high-specificity interaction involving an SH3 domain. The dynamic features are compared with those in the high-affinity, highly specific interaction between the SH3 domain of C-terminal Src kinase (Csk-SH3) and a proline-rich peptide from proline-enriched phosphatase (PEP). Both systems share common dynamic features especially in the canonical PxxP motif recognition surface where slow micro- to millisecond time scale dynamics persist on complex formation especially in several residues that are implicated in ligand recognition and in stabilizing the SH3 fold. These residues are highly conserved in SH3 domains. Ile505, which lies outside the PxxP recognition motif on p67(phox)SH3(C) and is key in conferring high specificity to the p67(phox)SH3(C)/Pf interaction, becomes more disordered upon complex formation. This behavior is similar to that seen in the residues that constitute the specificity surface in Csk-SH3.

Polymeric nanopores show unique transport properties and have attracted a great deal of scientific interest as a test system to study ionic and molecular transport at the nanoscale. By means of all-atom molecular dynamics, we simulated the ion dynamics inside polymeric polyethylene terephthalate nanopores. For this purpose, we established a protocol to assemble atomic models of polymeric material into which we sculpted a nanopore model with the key features of experimental devices, namely a conical geometry and a negative surface charge density. Molecular dynamics simulations of ion currents through the pore show that the protonation state of the carboxyl group of exposed polyethylene terephthalate residues have a considerable effect on ion selectivity, by affecting ionic densities and electrostatic potentials inside the nanopores. The role of high concentrations of Ca2+ ions on charge inversion effects, earlier reported in experiments, were investigated in detail.