scholarly journals Durotaxis of passive nanoparticles on elastic membranes

2021 ◽  
Author(s):  
Ivan Palaia ◽  
Alexandru Paraschiv ◽  
Vincent E Debets ◽  
Cornelis Storm ◽  
Andela Saric
Keyword(s):  
Chemical Processes ◽  
Elastic Membrane ◽  
Crucial Aspect ◽  
Physiological Processes ◽  
Average Motion ◽  
Elastic Membranes ◽  
Directional Motion ◽  
Direct Average ◽  
Dynamics Simulations ◽  
Transport Of Macromolecules

The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in non-uniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically non-uniform elastic membrane. We observe a non-monotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.

Shock loading of fixed flexible thread and orthotropic elastic membrane

2003 ◽  
Vol 3 ◽  
pp. 52-59
Author(s):  
S.S. Komarov ◽  
N.Yu. Tsvileneva ◽  
N.I. Miskaktin
Keyword(s):  
Numerical Methods ◽  
Dynamic Loading ◽  
Elastic Deformation ◽  
Numerical Algorithm ◽  
Shock Loading ◽  
Elastic Membrane ◽  
Wave Dynamics ◽  
Elastic Membranes ◽  
Pneumatic Structures

The main problems of the wave dynamics of flexible filaments and elastic membranes are solved. The reliability of the numerical algorithm proposed by the authors for calculating the elastic deformation of pneumatic structures under dynamic loading is confirmed when compared with the results of known studies obtained by analytical and numerical methods.

Bifurcation of rotating circular cylindrical elastic membranes

1980 ◽  
Vol 87 (2) ◽  
pp. 357-376 ◽  
Author(s):  
D. M. Haughton ◽  
R. W. Ogden
Keyword(s):  
Axial Force ◽  
Strain Energy ◽  
Elastic Strain Energy ◽  
Strain Energy Function ◽  
Angular Speed ◽  
Elastic Membrane ◽  
Axial Extension ◽  
End Conditions ◽  
Elastic Membranes ◽  
Realistic Choice

SummaryBifurcation from a finitely deformed circular cylindrical configuration of a rotating circular cylindrical elastic membrane is examined. It is found (for a physically realistic choice of elastic strain-energy function) that the angular speed attains a maximum followed by a minimum relative to the increasing radius of the cylinder for either a fixed axial extension or fixed axial force.At fixed axial extension (a) a prismatic mode of bifurcation (in which the cross-section of the cylinder becomes uniformly non-circular) may occur at a maximum of the angular speed provided the end conditions on the cylinder allow this; (b) axisyim-metric modes may occur before, at or after the angular speed maximum depending on the length of the cylinder and the magnitude of the axial extension; (c) an asymmetric or ‘wobble’ mode is always possible before either (a) or (b) as the angular speed increases from zero for any length of cylinder or axial extension. Moreover, ‘wobble’ occurs at lower angular speeds for longer cylinders.At fixed axial force the results are similar to (a), (b) and (c) except that an axisym-metric mode necessarily occurs between the turning points of the angular speed.

scholarly journals A Versatile and Robust Serine Protease Inhibitor Scaffold from Actinia tenebrosa

Marine Drugs ◽  
2019 ◽  
Vol 17 (12) ◽  
pp. 701 ◽  
Author(s):  
Xingchen Chen ◽  
Darren Leahy ◽  
Jessica Van Haeften ◽  
Perry Hartfield ◽  
Peter J. Prentis ◽  
...  
Keyword(s):  
Serine Protease ◽  
Protease Inhibitors ◽  
Serine Proteases ◽  
Inhibitor Design ◽  
Consensus Analysis ◽  
Fine Grained ◽  
Human Sequence ◽  
Physiological Processes ◽  
Definition Of ◽  
Dynamics Simulations

Serine proteases play pivotal roles in normal physiology and a spectrum of patho-physiological processes. Accordingly, there is considerable interest in the discovery and design of potent serine protease inhibitors for therapeutic applications. This led to concerted efforts to discover versatile and robust molecular scaffolds for inhibitor design. This investigation is a bioprospecting study that aims to isolate and identify protease inhibitors from the cnidarian Actinia tenebrosa. The study isolated two Kunitz-type protease inhibitors with very similar sequences but quite divergent inhibitory potencies when assayed against bovine trypsin, chymostrypsin, and a selection of human sequence-related peptidases. Homology modeling and molecular dynamics simulations of these inhibitors in complex with their targets were carried out and, collectively, these methodologies enabled the definition of a versatile scaffold for inhibitor design. Thermal denaturation studies showed that the inhibitors were remarkably robust. To gain a fine-grained map of the residues responsible for this stability, we conducted in silico alanine scanning and quantified individual residue contributions to the inhibitor’s stability. Sequences of these inhibitors were then used to search for Kunitz homologs in an A. tenebrosa transcriptome library, resulting in the discovery of a further 14 related sequences. Consensus analysis of these variants identified a rich molecular diversity of Kunitz domains and expanded the palette of potential residue substitutions for rational inhibitor design using this domain.

scholarly journals An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation

2010 ◽  
Vol 136 (4) ◽  
pp. 483-494 ◽  
Author(s):  
Ben Corry ◽  
Annette C. Hurst ◽  
Prithwish Pal ◽  
Takeshi Nomura ◽  
Paul Rigby ◽  
...  
Keyword(s):  
Patch Clamp ◽  
Conformational Changes ◽  
Brownian Dynamics ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Channel Structure ◽  
Paramagnetic Resonance ◽  
Physiological Processes ◽  
Lipid Environment ◽  
Dynamics Simulations

Mechanosensitive channels act as molecular transducers of mechanical force exerted on the membrane of living cells by opening in response to membrane bilayer deformations occurring in physiological processes such as touch, hearing, blood pressure regulation, and osmoregulation. Here, we determine the likely structure of the open state of the mechanosensitive channel of large conductance using a combination of patch clamp, fluorescence resonance energy transfer (FRET) spectroscopy, data from previous electron paramagnetic resonance experiments, and molecular and Brownian dynamics simulations. We show that structural rearrangements of the protein can be measured in similar conditions as patch clamp recordings while controlling the state of the pore in its natural lipid environment by modifying the lateral pressure distribution via the lipid bilayer. Transition to the open state is less dramatic than previously proposed, while the N terminus remains anchored at the surface of the membrane where it can either guide the tilt of or directly translate membrane tension to the conformation of the pore-lining helix. Combining FRET data obtained in physiological conditions with simulations is likely to be of great value for studying conformational changes in a range of multimeric membrane proteins.

Directional Motion of a Graphene Sheet on Graded MoS2–WSe2 Lateral Heterostructures

2019 ◽  
Vol 86 (6) ◽  
Author(s):  
Guang-Rong Han ◽  
Tienchong Chang ◽  
Jin-Wu Jiang
Keyword(s):  
Transition Metal ◽  
Graphene Sheet ◽  
Transition Metal Dichalcogenides ◽  
Interlayer Coupling ◽  
Underlying Mechanism ◽  
Initial Location ◽  
Directional Motion ◽  
Metal Dichalcogenides ◽  
Dynamics Simulations ◽  
Lateral Heterostructure

Directional motion is one of the most fundamental motions in the nature, which is driven by specific types of gradients. The transition metal dichalcogenides graded lateral heterostructure is a valuable semiconductor playing crucial roles in electronic and optoelectronic devices. This lateral heterostructure has a graded composition and is thus a promising candidate to drive possible directional motions. Here, we perform molecular dynamics simulations to demonstrate the directional motion of a graphene sheet on top of the MoS2–WSe2 graded lateral heterostructure. It is quite interesting that the direction for the diffusion is sensitive to the graphene sheet’s initial location, which is in two different regions. The graphene sheet diffuses in opposite directions for the initial location that falls in different regions. We derive an analytic formula for the interlayer coupling potential, which discloses the underlying mechanism for the dependence of the directional motion on the initial location of the graphene sheet. These results shall be varifiable by present experimental set ups and may be valuable for the application of the transition metal dichalcogenides graded lateral heterostructure in practical electronic devices.

A Kinetic Formulation of Reacting Molecular Dynamics

2016 ◽  
Author(s):  
Joseph L. Bass ◽  
Eric P. Fahrenthold
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Process Simulation ◽  
Chemical Processes ◽  
Detonation Products ◽  
Kinetic Formulation ◽  
Hamiltonian Methods ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Ab Initio Models

Macroscale, mesoscale, and ab initio models of reacting shock physics are based, in their most general forms, on rate law descriptions of the chemical processes of interest. Reacting molecular dynamics simulations, by contrast, typically employ potential functions to model chemical reactions. An alternative reacting molecular dynamics formulation, employing nonholonomic Hamiltonian methods, models bonding-debonding as a kinetic process. Simulation results using this method are compared with experiment, for energy release and detonation products in HMX. The molecular dynamics simulations may be used to develop a macroscale, adiabatic model of the detonation chemistry.

scholarly journals STOICHIOMETRY OF THE SODIUM PUMP-PHOSPHOLEMMAN REGULATORY COMPLEX

2021 ◽  
Author(s):  
Jaroslava Seflova ◽  
Nima R. Habibi ◽  
John Q. Yap ◽  
Sean R. Cleary ◽  
Xuan Fang ◽  
...  
Keyword(s):  
Structural Model ◽  
Alpha Subunit ◽  
Beta Subunits ◽  
Intact Cells ◽  
Sodium Potassium ◽  
Catalytic Subunits ◽  
Regulatory Subunits ◽  
Physiological Processes ◽  
Regulatory Complex ◽  
Dynamics Simulations

The sodium-potassium ATPase (NKA) establishes ion gradients that facilitate many physiological processes. In the heart, NKA activity is regulated by its interaction with phospholemman (PLM, FXYD1). Here we used a novel fluorescence lifetime-based assay to investigate the structure, stoichiometry, and affinity of the NKA-PLM regulatory complex. We observed concentration dependent association of the subunits of NKA-PLM regulatory complex, with avid association of the alpha subunit with the essential beta subunit followed by lower affinity alpha-alpha and alpha-PLM interactions. The data provide the first evidence that the regulatory complex is composed of two alpha subunits associated with two beta subunits, decorated with two PLM regulatory subunits in intact cells. Docking and molecular dynamics simulations generated a structural model of the complex that is consistent with our experimental observations. We propose that alpha-alpha subunit interactions support conformational coupling of the catalytic subunits, which may enhance NKA turnover rate. These observations provide insight into the pathophysiology of heart failure, wherein low NKA expression may be insufficient to support formation of the complete regulatory complex with stoichiometry (alpha-beta-PLM)2.

scholarly journals Ionic Liquids and Water: Hydrophobicity vs. Hydrophilicity

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7159
Author(s):  
Rita F. Rodrigues ◽  
Adilson A. Freitas ◽  
José N. Canongia Lopes ◽  
Karina Shimizu
Keyword(s):  
Ionic Liquid ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Aqueous Media ◽  
Liquid Solution ◽  
Chemical Processes ◽  
Processes And Reactions ◽  
High Hydrogen ◽  
Ionic Liquid Solution ◽  
Dynamics Simulations

Many chemical processes rely extensively on organic solvents posing safety and environmental concerns. For a successful transfer of some of those chemical processes and reactions to aqueous media, agents acting as solubilizers, or phase-modifiers, are of central importance. In the present work, the structure of aqueous solutions of several ionic liquid systems capable of forming multiple solubilizing environments were modeled by molecular dynamics simulations. The effect of small aliphatic chains on solutions of hydrophobic 1-alkyl-3-methylimidazolium bis(trifluoromethyl)sulfonylimide ionic liquids (with alkyl = propyl [C3C1im][NTf2], butyl [C4C1im][NTf2] and isobutyl [iC4C1im][NTf2]) are covered first. Next, we focus on the interactions of sulphonate- and carboxylate-based anions with different hydrogenated and perfluorinated alkyl side chains in solutions of [C2C1im][CnF2n+1SO3], [C2C1im][CnH2n+1SO3], [C2C1im][CF3CO2] and [C2C1im][CH3CO2] (n = 1, 4, 8). The last system considered is an ionic liquid completely miscible with water that combines the cation N-methyl-N,N,N-tris(2-hydroxyethyl)ammonium [N1 2OH 2OH 2OH]+, with high hydrogen-bonding capability, and the hydrophobic anion [NTf2]–. The interplay between short- and long-range interactions, clustering of alkyl and perfluoroalkyl tails, and hydrogen bonding enables a wealth of possibilities in tailoring an ionic liquid solution according to the needs.

scholarly journals Density, Enthalpy of Vaporization and Local Structure of Neat N-Alkane Liquids

Liquids ◽  
2021 ◽  
Vol 1 (1) ◽  
pp. 47-59
Author(s):  
Gerrick E. Lindberg ◽  
Joseph L. Baker ◽  
Jennifer Hanley ◽  
William M. Grundy ◽  
Caitlin King
Keyword(s):  
Chemical Processes ◽  
Distribution Functions ◽  
Average Absolute Deviation ◽  
Average Deviation ◽  
Absolute Deviation ◽  
Amber Force Field ◽  
Local Structures ◽  
Ideal Solution Behavior ◽  
Experimental Values ◽  
Dynamics Simulations

The properties of alkanes are consequential for understanding many chemical processes in nature and industry. We use molecular dynamics simulations with the Amber force field GAFF2 to examine the structure of pure liquids at each respective normal boiling point, spanning the 15 n-alkanes from methane to pentadecane. The densities predicted from the simulations are found to agree well with reported experimental values, with an average deviation of 1.9%. The enthalpies of vaporization have an average absolute deviation from experiment of 10.4%. Radial distribution functions show that short alkanes have distinct local structures that are found to converge with each other with increasing chain length. This provides a unique perspective on trends in the n-alkane series and will be useful for interpreting similarities and differences in the n-alkane series as well as the breakdown of ideal solution behavior in mixtures of these molecules.

Large deformation possible in every isotropic elastic membrane

1977 ◽  
Vol 287 (1341) ◽  
pp. 145-187 ◽  
Keyword(s):  
Strain Energy ◽  
Closed Surface ◽  
Elastic Membrane ◽  
Energy Response ◽  
Normal Surface ◽  
Metric Tensor ◽  
Alternative Description ◽  
Special Cases ◽  
Static Solutions ◽  
Elastic Membranes

This paper is concerned with static solutions of finitely deformed elastic membranes regarded as thin shells. It deals with deformations that can be maintained, in the absence of body force, in every isotropic elastic membrane by the application of edge loads and/or uniform normal surface loads on the major surfaces of the thin shell-like body. The solutions, which are valid for both compressible and incompressible materials, are obtained with the use of a strain energy response function which depends on the metric tensor of the membrane in its deformed configuration. The main results are summarized by several theorems and their corollaries in accordance with three mutually exclusive cases for which the initial undeformed surface of the membrane (which may be a sector of a complete or closed surface) is, respectively, developable, spherical and a surface of variable Gaussian curvature satisfying certain differential criteria. The corresponding deformed surfaces are, respectively, a plane or a right circular cylinder, a sphere and a surface of constant mean curvature. These results are exhaustive in that they represent all finite deformation solutions possible in every isotropic elastic material characterized by the strain energy response mentioned above. Also discussed are some special cases of the general results and several families of solutions in terms of an alternative description which should be useful in application and which permit easy interpretations.

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