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Search results for: molecular-dynamics
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A Strategy to Locate Fixed Points and Global Perturbations of ODE’s: Mixing Topology with Metric Conditions
PublicationIn this paper we discuss a topological treatment for the planar system z' = f (t, z) + g(t, z) where f and g are T -periodic in time and g(t, z) is bounded. Namely, we study the effect of g(t, z) in two different frameworks: isochronous centers and time periodic systems having subharmonics. The main tool employed in the proofs consists of a topological strategy to locate fixed points in the class of orientation preserving embedding...
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Recent Developments in Data-Assisted Modeling of Flexible Proteins
PublicationMany proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...
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Equivalent Single Layer Models in Free Vibration Analysis of Laminated Multi-Layered Plates
PublicationThe performance of selected equivalent single-layer (ESL) models is evaluated within several classical benchmark tests for small amplitude free vibration analysis of multi-layered plates. The authors elaborated their own Finite Element software based on the first-order shear deformation (FOSD) theory with some modifications incorporated including a correction of the transverse shear stiffness and an application of zigzag type functions....
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Physical, chemical and biochemical properties of Western Siberia Sphagnum and Carex peat soils
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Dynamic inequalities and equations of Volterra type on time scales
PublicationPraca dotyczy całkowo-różniczkowych równań dynamicznych typu Volterry z warunkami początkowymi. Stosując twierdzenie Banacha o punkcie stałym pokazano istnienie jedynego rozwiązania liniowego równania dynamicznego. Stosując metodę iteracji monotonicznych pokazano istnienie rozwiązań ekstremalnych dla problemów nieliniowych. Badano też nierówności dynamiczne. Praca zawiera również uwagi dotyczące zagadnień różniczkowych i różnicowych.
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Positive solutions to boundary value problems for impulsive second-order differential equations
PublicationIn this paper, we discuss four-point boundary value problems for impulsive second-order differential equations. We apply the Krasnoselskii's fixed point theorem to obtain sufficient conditions under which the impulsive second-order differential equations have positive solutions. An example is added to illustrate theoretical results.
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Positive solutions to second order four-point impulsive problems with deviating arguments
PublicationStosując tw. Leggetta-Williamsa, podano warunki dostateczne na istnienie dodatnich rozwiązań dla czteropunktowych problemów brzegowych dla równań różniczkowych rzędu drugiego z odchylonymi argumentami. Dyskutowane były problemy gdy argument odchylony był typu opóźnionego lub wyprzedzonego.
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Boundary value problems for dynamic equations of Volterra type on time scales
PublicationPraca dotyczy równań i nierówności dla problemów dynamicznych typu Volterry. Podano warunki dostateczne na istnienie ekstremalnych rozwiązań w obszarze ograniczonym przez dolne i górne rozwiązania. Praca zawiera również pewne uwagi dla konkretnych zagadnień różniczkowych i dyskretnych.
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On integro-differential equations with delayed arguments
PublicationPraca dotyczy problemów różniczkowo-całkowych z warunkami początkowymi oraz brzegowymi typu okresowego. Podano warunki na istnienie i jednoznaczność rozwiązania. Badania dotyczyły również nierówności różniczkowo-całkowych z argumentami typu opóżnionego. Podano przykłady, które mogą mieć zastosowanie w problemach inżynierskich.
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Vibration Diagnostics of Rolling Mills Based on Nonlinear Effects in Dynamics
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Determinants of Directionality and Efficiency of the ATP Synthase Fo Motor at Atomic Resolution
PublicationFo subcomplex of ATP synthase is a membrane-embedded rotary motor that converts proton motive force into mechanical energy. Despite a rapid increase in the number of high-resolution structures, the mechanism of tight coupling between proton transport and motion of the rotary c-ring remains elusive. Here, using extensive all-atom free energy simulations, we show how the motor’s directionality naturally arises from the interplay...
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Molecular mechanism of proton-coupled ligand translocation by the bacterial efflux pump EmrE
PublicationThe current surge in bacterial multi-drug resistance (MDR) is one of the largest challenges to public health, threatening to render ineffective many therapies we rely on for treatment of serious infections. Understanding different factors that contribute to MDR is hence crucial from the global “one health” perspective. In this contribution, we focus on the prototypical broad-selectivity proton-coupled antiporter EmrE, one of the...
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Solubility of Methane in Water: Some Useful Results for Hydrate Nucleation
PublicationIn this paper, the solubility of methane in water along the 400 bar isobar is determined by computer simulations using the TIP4P/Ice force field for water and a simple LJ model for methane. In particular, the solubility of methane in water when in contact with the gas phase and the solubility of methane in water when in contact with the hydrate has been determined. The solubility of methane in a gas–liquid system decreases as temperature...
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How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
PublicationTarget search as performed by DNA-binding proteins is a complex process, in which multiple factors contribute to both thermodynamic discrimination of the target sequence from overwhelmingly abundant off-target sites and kinetic acceleration of dynamic sequence interrogation. TRF1, the protein that binds to telomeric tandem repeats, faces an intriguing variant of the search problem where target sites are clustered within short fragments...