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Search results for: BIOMOLECULAR INTERACTIONS
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Effects of interactions between variation in dopaminergic genes, traumatic life events, and anomalous self-experiences on psychosis proneness: Results from a cross-sectional study in a nonclinical sample
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Discussion on “Dynamic soil-structure interaction: A three-dimensional numerical approach and its application to the Lotung case study”. Poor performance of the HSS model
PublicationThe Hardening Soil Small (HSS) is a constitutive model being extension to the well established Hardening Soil Model (HS) accounting for the nonlinearity of small strain stiffness. It is implemented in commercial finite element computer codes for geotechnical analyses and used widely in research and design. The article deals with a problem known as overshooting after very small load reversals. It induces much higher stiffness than...
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Least absolute shrinkage and selection operator and dimensionality reduction techniques in quantitative structure retention relationship modeling of retention in hydrophilic interaction liquid chromatography
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The interaction between cuticle free fatty acids (FFAs) of the cockroaches Blattella germanica and Blatta orientalis and hydrolases produced by the entomopathogenic fungus Conidiobolus coronatus
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Influence of amino acid sequence on the interaction of short peptides containing 3-[2-(9-anthryl)benzoxazol-5-yl]-alanine with β-cyclodextrin
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Balal Yousaf Dr.
PeopleBalal Yousaf currently works as a Professor at the Silesian University of Technology, Gliwice, Poland. He has an academic background in Environmental Geochemistry & Pollution. His research interests include Soil and Water Remediation, Transformation Mechanism and Fate of Environmental Contaminants, Minerals Interaction with Environmental Contaminants, Green Synthesis, Biowaste Conversion, Bioenergy and Environmental Pollution...
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Comment on “Entanglement of two interacting bosons in a two-dimensional isotropic harmonic trap” [Phys. Lett. A 373 (2009) 3833]
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Interaction Design & Architecture(s)
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Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: Molecular dynamics study of a pair of methane molecules in water at various temperatures
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Differential Response of MDA-MB-231 and MCF-7 Breast Cancer Cells to In Vitro Inhibition with CTLA-4 and PD-1 through Cancer-Immune Cells Modified Interactions
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Marcin Sikorski prof. dr hab. inż.
PeopleMarcin Sikorski is a professor at the Department of Informatics in Management at the Faculty of Management and Economics of the Gdańsk University of Technology. Earlier he had numerous fellowships in academic institutions, among others in Germany (Universities in Bonn and in Heidelberg), Switzerland (ETH Zurich), the Netherlands (TU Eindhoven) and the USA (Harvard University). Professor Sikorski is a representative of Poland in...
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Krzysztof Jan Kaliński prof. dr hab. inż.
PeopleKrzysztof J. Kaliński completed his MSc study at Gdańsk University of Technology (GUT) Faculty of Production Engineering (1980, result – get a first). He obtained PhD at GUT Faculty of Machine Building (1988, result – get a first), DSc at GUT Faculty of Mechanical Engineering (ME) (2002, result – get a first), and professor’s title – w 2013 r. In 2015 r. he became full professor.His research area includes: theoretical and applied...
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Impact of inorganic ions and pH variations on toxicity and endocrine potential of selected environmentally relevant pharmaceuticals
PublicationAssessment of the impact of pharmaceutical residues on living organisms is a very complex subject. Apart from taking into account the toxicity of individual compounds, environmental factors should also be taken into account. In this paper, attempts were made to assess the impact of coexisting inorganic ions and changes in pH on the toxicity of ten selected pharmaceuticals. Two bioassays were used to measure the estrogenic and androgenic...
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Supramolecular structures formed by 2-aminopyridine derivatives. Part I. Hydrogenbonding networks via N-H...N interactions and the conformational polymorphism of N,N´-bis(2-piridyl)aryldiamines
PublicationOtrzymano serię N,N´-bis(2-pirydylo)arylodiamin w postaci monokryształów. Zgodnie z oczekiwaniami, powstawały dwie odmiany polimorficzne. Forma EE z układem wiązań R22(8) figuruje jako jednowymiarowe taśmy. Stwierdzono, że ugrupowanie 2-aminopirydylowe stanowi synton supramolekularny za pomocą którego można projektować struktury w ciele stałym. Właściwości tego syntonu były badane z wykorzystaniem metod dyfrakcyjnych oraz spektroskopii...
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Understanding ion–ion and ion–solvent interactions in aqueous solutions of morpholinium ionic liquids with N-acetyl-L-alaninate anion through partial molar properties and molecular dynamics simulations
PublicationAmino acid ionic liquids (AAILs) provide a low toxicity, biodegradable alternative to conventional ionic liquids, while also maintaining solubility in water. Densities and sound velocities of aqueous solutions of four amino acid ionic liquids (AAILs), based on the N-alkyl-N-methylmorpholinium ([Mor1,R], R = 2, 3, 6, 8) cation and N-acetyl-L-alaninate ([N-Ac-L-Ala]) anion were measured at T = (293.15–313.15) K and at atmospheric...
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Au nanoparticles identifiction with the use of AFM Volta potential mapping
Open Research DataThe specific physical, chemical and electrochemical electrical properties of gold nanoparticles have led to their extensive use as high-performance chemical and biochemical sensors. The described properties relate to surface plasmon resonance, fluorescence quenching or enhancement, high electrical conductivity and light scattering. The described nanoparticles...
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Chemical Aspects of Biological Activity of Isothiocyanates and Indoles, the Products of Glucosinolate Decomposition
PublicationThere is growing evidence that cancer chemoprevention employing natural, bioactive compounds may halt or at least slow down the different stages of carcinogenesis. A particularly advantageous effect is attributed to derivatives of sulfur-organic phytochemicals, such as glucosinolates (GLs) synthesized mainly in Brassicaceae plant family. GLs are hydrolysed enzymatically to bioactive isothiocyanates (ITC) and indoles, which exhibit strong...
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Mechanism of recognition of parallel G-quadruplexes by DEAH/RHAU helicase DHX36 explored by molecular dynamics simulations
PublicationBecause of high stability and slow unfolding rates of G-quadruplexes (G4), cells have evolved specialized helicases that disrupt these non-canonical DNA and RNA structures in an ATP-dependent manner. One example is DHX36, a DEAH-box helicase, which participates in gene expression and replication by recognizing and unwinding parallel G4s. Here, we studied the molecular basis for the high affinity and specificity of DHX36 for parallel-type...
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Analysis of Reconstituted Tripartite Complex Supports Avidity-based Recruitment of Hsp70 by Substrate Bound J-domain Protein
PublicationHsp70 are ubiquitous, versatile molecular chaperones that cyclically interact with substrate protein(s). The initial step requires synergistic interaction of a substrate and a J-domain protein (JDP) cochaperone, via its J-domain, with Hsp70 to stimulate hydrolysis of its bound ATP. This hydrolysis drives conformational changes in Hsp70 that stabilize substrate binding. However, because of the transient nature of substrate and JDP...
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Initial performance evaluation of a high resolution Albira small animal positron emission tomography scanner with monolithic crystals and depth-of-interaction encoding from a user's perspective
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Mutual Interaction between Temperature and DO Set Point on AOB and NOB Activity during Shortcut Nitrification in a Sequencing Batch Reactor in Terms of Energy Consumption Optimization
PublicationRecently, many wastewater treatment plants (WWTPs) have had to deal with serious problems related to the restrictive requirements regarding the euent quality, as well as significant energy consumption associated with it. In this situation, mainstream deammonification and/or shortened nitrification-denitrification via nitrite (so-called “nitrite shunt”) is a new promising strategy. This study shows the mechanisms and operating conditions...
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Simple Physics-Based Analytical Formulas for the Potentials of Mean Force for the Interaction of Amino Acid Side Chains in Water. IV. Pairs of Different Hydrophobic Side Chains
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Comparison of hydrophilic interaction and reversed phase liquid chromatography coupled with tandem mass spectrometry for the determination of eight artificial sweeteners and common steviol glycosides in popular beverages
PublicationHydrophilic interaction liquid chromatography (HILIC) coupled with tandem mass spectrometry (MS/MS) was used to separate artificial and natural sweeteners approved for use in European Union (EU). Among three tested HILIC columns (BlueOrchid PAL-HILIC, Ascentis Express Si and Acclaim™ Trinity™ P2) the last one was selected for the development of HILIC method due to the best results obtained with it. Early eluting and coeluting compounds...
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Coupled Urban Areas Inundation Model with Interaction Between Storm Water System and Surface Flow - Case Study of Sea Level Impact on Seaside Areas Flooding
PublicationInundations are becoming more frequent than ever. What is connected with increasing area of impervious surface in cities. This makes predicting urban flooding and its scale especially important. At the seaside we observe additional conditions such as sea level that makes accurate numerical modelling of issue even harder. With complex approach to the matter which is simultaneous calculation of storm water conduit flow and overland...
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Dipole-bound anions supported by charge-transfer interaction: Anionic states of HnF3?nN ? BH3 and H3N ? BHnF3?n (n = 0, 1, 2, 3)
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Low-energy positron scattering from gas-phase pyrimidine: A quantum treatment of the dynamics and a comparison with experiments
PublicationWe are reporting detailed quantum scattering calculations that describe the diffusion of a beam of low-energy positrons interacting with the pyrimidine target as a gas-phase partner. The calculations have employed an essentially ab initio model for the short-range correlation interaction and for the electrostatic interaction of an impinging positron and the electron+nuclear structure of the target molecule at its equilibrium geometry.
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Sylwester Kaczmarek dr hab. inż.
PeopleSylwester Kaczmarek received his M.Sc in electronics engineering, Ph.D. and D.Sc. in switching and teletraffic science from the Gdansk University of Technology, Gdansk, Poland, in 1972, 1981 and 1994, respectively. His research interests include: IP QoS and GMPLS and SDN networks, switching, QoS routing, teletraffic, multimedia services and quality of services. Currently, his research is focused on developing and applicability...
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Development of polyurethanes for bone repair
PublicationThe purpose of this paper is to review recent developments on polyurethanes aimed at the design, synthesis, modifications, and biological properties in the field of bone tissue engineering. Different polyurethane systems are presented and discussed in terms of biodegradation, biocompatibility and bioactivity. A comprehensive discussion is provided of the influence of hard to soft segments ratio, catalysts, stiffness and hydrophilicity...
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A Special Section on Intelligent User Interfaces in Healthcare (IUIH)
PublicationA concept of interface has evolved from the first appearance in the form of a command line interface to the established use of direct manipulation or WIMP (windows, icons, menus and pointing) interfaces in nearly all applications. Intelligent user interfaces (IUI) form a subfield of Human-Computer Interaction research. Optimal human-computer interactions are defined as ones where users are able to perform complex tasks more quickly...
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Prediction of maximum tensile stress in plain-weave composite laminates with interacting holes via stacked machine learning algorithms: A comparative study
PublicationPlain weave composite is a long-lasting type of fabric composite that is stable enough when being handled. Open-hole composites have been widely used in industry, though they have weak structural performance and complex design processes. An extensive number of material/geometry parameters have been utilized for designing these composites, thereby an efficient computational tool is essential for that purpose. Different Machine Learning...
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Cooperativity of Halogen- and Chalcogen-Bonding Interactions in the Self-Assembly of 4‑Iodoethynyl- and 4,7-Bis(iodoethynyl)benzo-2,1,3-chalcogenadiazoles: Crystal Structures, Hirshfeld Surface Analyses, and Crystal Lattice Energy Calculations
PublicationSeveral new 4-iodoethynyl- and 4,7-bis- (iodoethynyl)benzo-2,1,3-chalcogenadiazoles were prepared, and a comprehensive analysis of the most prominent secondary bonding interactions responsible for the crystal self-assembly was performed using X-ray diffraction. The presence of both the iodoethynyl and chalcogenadiazole moieties allows an evaluation of the preference of these molecules to aggregate through either chalcogen- or halogen-bonding...
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N-doped carbon nanospheres as selective fluorescent probes for mercury detection in contaminated aqueous media: chemistry, fluorescence probing, cell line patterning, and liver tissue interaction
PublicationA precise nano-scale biosensor was developed here to detect Hg2+ in aqueous media. Nitrogen-doped carbon nanospheres (NCS) created from the pyrolysis of melamine–formaldehyde resin were characterized by FESEM, XRD, Raman spectra, EDS, PL, UV–vis spectra, and N2 adsorption–desorption, and were used as a highly selective and sensitive probe for detecting Hg2+ in aqueous media. The sensitivity of NCS to Hg2+ was evaluated by photoluminescence...
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Continuum wave functions for estimating the electric dipole moment: Calculation based on a multiconfiguration Dirac-Hartree-Fock approximation
PublicationThe multiconfiguration Dirac-Hartree-Fock method is employed to calculate the continuum electron wave functions, which are then used to estimate their contribution to the atomic electric dipole moment (EDM) of 129Xe. The EDM arises from (P,T)-odd electron-nucleon tensor-pseudotensor and pseudoscalar-scalar interactions, the nuclear Schiff moment, the interaction of the electron electric dipole moment with nuclear magnetic moments,...
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Up-to-date strategies and future trends towards the extraction and purification of Capsaicin: A comprehensive review
PublicationBackground According to the current need of manufacturing healthier products, food companies are seeking specific biomolecules that may offer additional added value (i.e., biological activities) to the new food formulations. Capsaicin, as the pungent ingredient of chili peppers, has become so far one of the target biomolecules explored since the 1950s. There is evidence demonstrating that capsaicin exhibits important biological...
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The good, the bad, and the ugly: space use and intraguild interactions among three opportunistic predators—cat (Felis catus), dog (Canis lupus familiaris), and red fox (Vulpes vulpes)—under human pressure
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Crystallographic study of self-organization in the solid state including quasi-aromatic pseudo-ring stacking interactions in 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea and 1-benzoyl-3-(2-hydroxypropyl)thiourea
Publication1-Benzoylthioureas contain both carbonyl and thiocarbonyl functional groups and are of interest for their biological activity, metal coordination ability and involvement in hydrogen-bond formation. Two novel 1-benzoylthiourea derivatives, namely 1-benzoyl-3-(3,4-dimethoxyphenyl)thiourea, C₁₆H₁₆N₂O₃S, (I), and 1-benzoyl-3-(2-hydroxypropyl)thiourea, C₁₁H₁₄N₂O₂S, (II), have been synthesized and characterized. Compound (I) crystallizes...
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In silico modelling for predicting the cationic hydrophobicity and cytotoxicity of ionic liquids towards the Leukemia rat cell line, Vibrio fischeri and Scenedesmus vacuolatus based on molecular interaction potentials of ions
PublicationIn this study we present prediction models for estimating in silico the cationic hydrophobicity and the cytotoxicity (log [1/EC50]) of ionic liquids (ILs) towards the Leukemia rat cell line (IPC-81), the marine bacterium Vibrio fischeri and the limnic green algae Scenedesmus vacuolatus using linear free energy relationship (LFER) descriptors computed by COSMO calculations. The LFER descriptors used for the prediction model (i.e....
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Lower rim substituted tert-Butylcalix[4]arenes. Part 13. Interaction of calix-hydroxamates with Fe(III) and Pb(II); studies in ion-selective membrane electrodes (ISE)
PublicationPrzedmiotem pracy są badania oddziaływań pomiędzy trzema wybranymi hydroksamowymi pochodnymi t-butylo-kaliks[4]arenu i jonami metali z wykorzystaniem membranowych elektrod jonoselektywnych (ISE). Elektrody zawierające jako materiał aktywny wymienione związki jonoforowe charakteryzują się nernstowskim nachyleniem i szerokim zakresem liniowości na jony Pb(II), a także dobrą selektywnością na jony Pb(II)w stosunku do jonów UO2(II),...
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
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“Dilute & Shoot” approach for rapid determination of trace amounts of nicotine in zero-level e-liquids by reversed phase liquid chromatography and hydrophilic interactions liquid chromatography coupled with tandem mass spectrometry-electrospray ionization
PublicationTwo analytical procedures are proposed where HILIC and RPLC techniques are coupled with tandem mass spectrometry detection for rapid determination of trace amounts of nicotine in zero-level liquids for electronic cigarettes. Samples are prepared on the basis of the approach “dilute & shoot” which makes this important step quick and not complicated. The chromatographic separation was carried out on a Zorbax XDB column (RPLC method)...
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DYNAMIC ANALYSIS OF THE IMPACT OF VIBRATION ON HISTORICAL BUILDINGS - AN OWN PROJECT OF EXTERNAL STAIRCASE
PublicationThis article presents numerical simulations that concern modeling of interaction of the external staircase’s construction with the observation deck on historic water tower located at Gdansk University of Technology. The interaction occurring according to various methods of the staircase's construction support on the wall of the historic tower was compared. The external staircase that allows for entering onto the monument was subjected...
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Down-regulation of DNA topoisomerase IIalpha leads to prolonged cell cycle transit in G2 and early M phases and increased survival to microtubule-interacting agents
PublicationInhibitory polimeryzacji mikrotubul wykazują preferencyjną toksyczność wobec komórek mitotycznych. W ramach tego projektu badaliśmy czy oporność komórek ludzkich białaczek na inhibitor mikrotubul, winkrystynę, prowadzi do zmian w regulacji progresji cyklu komórkowego. Nasze wyniki wskazują, że oporności na winkrystynę towarzyszą zmiany w długości fazy G2 i M w nieobecności i obecności inhibitora wrzeciona mitotycznego, nokodazolu....
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Dariusz Dąbrowski dr hab. inż.
PeopleDariusz Dąbrowski graduated from the Faculty of Shipbuilding at Gdańsk University of Technology and in 1987 began working at the university as an assistant in the Department of Shipbuilding Industry Organization within the then Institute of Organization and Design of Production Systems. In 1990, he went on a TEMPUS scholarship from the EU and spent 14 months at the University of Sheffield, where he participated in the Master of...
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Tadeusz Stolarski prof. dr hab. inż.
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Structure-activity relationship study of a small cyclic peptide H-c[Lys-Pro-Glu]-Arg-OH: a potent inhibitor of Vascular Endothelial Growth Factor interaction with Neuropilin-1
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Multi-state multi-reference Møller-Plesset second-order perturbation theory for molecular calculations
PublicationThis work presents multi‐state multi‐reference Møller–Plesset second‐order perturbation theory as a variant of multi‐reference perturbation theory to treat electron correlation in molecules. An effective Hamiltonian is constructed from the first‐order wave operator to treat several strongly interacting electronic states simultaneously. The wave operator is obtained by solving the generalized Bloch equation within the first‐order...
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Longitudinal drug synergy assessment using convolutional neural network image-decoding of glioblastoma single-spheroid cultures
PublicationAbstract Background In recent years, drug combinations have become increasingly popular to improve therapeutic outcomes in various diseases, including difficult to cure cancers such as the brain cancer glioblastoma. Assessing the interaction between drugs over time is critical for predicting drug combination effectiveness and minimizing the risk of therapy resistance. However, as viability readouts of drug combination experiments...
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Anion–cation interactions in a series of salts with substituted Hphen, Hbpy and H2bpy cations and [W(CN)8]4− anion: polymer with “super-short” N–H⋯N hydrogen bridges containing exclusively anions and H+
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Sharp transitions in low-number quantum dots Bayesian magnetometry
PublicationWe consider Bayesian estimate of static magnetic field, characterized by a prior Gaussian probability distribution, in systems of a few electron quantum dot spins interacting with infinite temperature spin environment via hyperfine interaction. Sudden transitions among optimal states and measurements are observed. Usefulness of measuring occupation levels is shown for all times of the evolution, together with the role of entanglement...
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Continuum contact model for friction between graphene sheets that accounts for surface anisotropy and curvature
PublicationUnderstanding the interaction mechanics between graphene layers and co-axial carbon nanotubes (CNTs) is essential for modeling graphene and CNT-based nanoelectromechanical systems. This work proposes a new continuum contact model to study interlayer interactions between curved graphene sheets. The continuum model is calibrated and validated using molecular dynamics (MD) simulations. These are carried out employing the reactive...