scholarly journals Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff-Love kinematics and revealed by a three dimensional computational framework

2021 ◽  
Author(s):  
Debabrata Auddya ◽  
Xiaoxuan Zhang ◽  
Rahul Gulati ◽  
Ritvik Vasan ◽  
Krishna Garikipati ◽  
...  
Keyword(s):  
Symmetry Breaking ◽  
Lipid Bilayers ◽  
Morphological Changes ◽  
Dimensional Space ◽  
Wide Spectrum ◽  
Three Dimensional ◽  
Mathematical Basis ◽  
Membrane Deformation ◽  
Membrane Geometry ◽  
Organelle Morphology

AbstractBiomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modeling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modeling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff-Love thin-shell kinematics, Helfrich-energy based mechanics, and state-of-the-art numerical techniques for modeling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modeling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a 3D space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modeling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a “phase diagram” for its symmetric and broken-symmetry states.

scholarly journals Biomembranes undergo complex, non-axisymmetric deformations governed by Kirchhoff–Love kinematicsand revealed by a three-dimensional computational framework

2021 ◽  
Vol 477 (2255) ◽  
Author(s):  
Debabrata Auddya ◽  
Xiaoxuan Zhang ◽  
Rahul Gulati ◽  
Ritvik Vasan ◽  
Krishna Garikipati ◽  
...  
Keyword(s):  
Symmetry Breaking ◽  
Lipid Bilayers ◽  
Morphological Changes ◽  
Dimensional Space ◽  
Wide Spectrum ◽  
Three Dimensional ◽  
Mathematical Basis ◽  
Membrane Deformation ◽  
Membrane Geometry ◽  
Three Dimensional Space

Biomembranes play a central role in various phenomena like locomotion of cells, cell-cell interactions, packaging and transport of nutrients, transmission of nerve impulses, and in maintaining organelle morphology and functionality. During these processes, the membranes undergo significant morphological changes through deformation, scission, and fusion. Modelling the underlying mechanics of such morphological changes has traditionally relied on reduced order axisymmetric representations of membrane geometry and deformation. Axisymmetric representations, while robust and extensively deployed, suffer from their inability to model-symmetry breaking deformations and structural bifurcations. To address this limitation, a three-dimensional computational mechanics framework for high fidelity modelling of biomembrane deformation is presented. The proposed framework brings together Kirchhoff–Love thin-shell kinematics, Helfrich-energy-based mechanics, and state-of-the-art numerical techniques for modelling deformation of surface geometries. Lipid bilayers are represented as spline-based surface discretizations immersed in a three-dimensional space; this enables modelling of a wide spectrum of membrane geometries, boundary conditions, and deformations that are physically admissible in a three-dimensional space. The mathematical basis of the framework and its numerical machinery are presented, and their utility is demonstrated by modelling three classical, yet non-trivial, membrane deformation problems: formation of tubular shapes and their lateral constriction, Piezo1-induced membrane footprint generation and gating response, and the budding of membranes by protein coats during endocytosis. For each problem, the full three-dimensional membrane deformation is captured, potential symmetry-breaking deformation paths identified, and various case studies of boundary and load conditions are presented. Using the endocytic vesicle budding as a case study, we also present a ‘phase diagram’ for its symmetric and broken-symmetry states.

scholarly journals Distance Between Two Circles In Any Number Of Dimensions Is A Vector Ellipse

2021 ◽  
Author(s):  
Asli Pinar Tan
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Mathematical Basis ◽  
Multiple Dimensions ◽  
Special Cases ◽  
Position Data ◽  
Gravitational Pull ◽  
Elliptical Motion ◽  
The Universe ◽  
Moving Bodies

Based on measured astronomical position data of heavenly objects in the Solar System and other planetary systems, all bodies in space seem to move in some kind of elliptical motion with respect to each other, whereas objects follow parabolic escape orbits while moving away from Earth and bodies asserting a gravitational pull, and some comets move in near-hyperbolic orbits when they approach the Sun. In this article, it is first mathematically proven that the “distance between points on any two different circles in three-dimensional space” is equivalent to the “distance of points on a vector ellipse from another fixed or moving point, as in two-dimensional space.” Then, it is further mathematically demonstrated that “distance between points on any two different circles in any number of multiple dimensions” is equivalent to “distance of points on a vector ellipse from another fixed or moving point”. Finally, two special cases when the “distance between points on two different circles in multi-dimensional space” become mathematically equivalent to distances in “parabolic” or “near-hyperbolic” trajectories are investigated. Concepts of “vector ellipse”, “vector hyperbola”, and “vector parabola” are also mathematically defined. The mathematical basis derived in this Article is utilized in the book “Everyhing Is A Circle: A New Model For Orbits Of Bodies In The Universe” in asserting a new Circular Orbital Model for moving bodies in the Universe, leading to further insights in Astrophysics.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

Diffraction contrast of dislocations in icosahedral quasicrystals

1990 ◽  
Vol 48 (4) ◽  
pp. 454-455
Author(s):  
K. Urban ◽  
Z. Zhang ◽  
M. Wollgarten ◽  
D. Gratias
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Complete Characterization ◽  
Extinction Condition ◽  
Burgers Vector ◽  
Diffraction Contrast ◽  
Lattice Geometry ◽  
Reference Space ◽  
Icosahedral Quasicrystals ◽  
The One

Recently dislocations have been observed by electron microscopy in the icosahedral quasicrystalline (IQ) phase of Al65Cu20Fe15. These dislocations exhibit diffraction contrast similar to that known for dislocations in conventional crystals. The contrast becomes extinct for certain diffraction vectors g. In the following the basis of electron diffraction contrast of dislocations in the IQ phase is described. Taking account of the six-dimensional nature of the Burgers vector a “strong” and a “weak” extinction condition are found.Dislocations in quasicrystals canot be described on the basis of simple shear or insertion of a lattice plane only. In order to achieve a complete characterization of these dislocations it is advantageous to make use of the one to one correspondence of the lattice geometry in our three-dimensional space (R3) and that in the six-dimensional reference space (R6) where full periodicity is recovered . Therefore the contrast extinction condition has to be written as gpbp + gobo = 0 (1). The diffraction vector g and the Burgers vector b decompose into two vectors gp, bp and go, bo in, respectively, the physical and the orthogonal three-dimensional sub-spaces of R6.

Flavin radicals, conformational sampling and robust design principles in interprotein electron transfer: the trimethylamine dehydrogenase-electron-transferring flavoprotein complex

2004 ◽  
Vol 71 ◽  
pp. 1-14
Author(s):  
David Leys ◽  
Jaswir Basran ◽  
François Talfournier ◽  
Kamaldeep K. Chohan ◽  
Andrew W. Munro ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Kinetic Studies ◽  
Molecular Assembly ◽  
Conformational Sampling ◽  
Trimethylamine Dehydrogenase ◽  
Key Residues ◽  
Electron Transferring Flavoprotein ◽  
Electron Transfer Complex

TMADH (trimethylamine dehydrogenase) is a complex iron-sulphur flavoprotein that forms a soluble electron-transfer complex with ETF (electron-transferring flavoprotein). The mechanism of electron transfer between TMADH and ETF has been studied using stopped-flow kinetic and mutagenesis methods, and more recently by X-ray crystallography. Potentiometric methods have also been used to identify key residues involved in the stabilization of the flavin radical semiquinone species in ETF. These studies have demonstrated a key role for 'conformational sampling' in the electron-transfer complex, facilitated by two-site contact of ETF with TMADH. Exploration of three-dimensional space in the complex allows the FAD of ETF to find conformations compatible with enhanced electronic coupling with the 4Fe-4S centre of TMADH. This mechanism of electron transfer provides for a more robust and accessible design principle for interprotein electron transfer compared with simpler models that invoke the collision of redox partners followed by electron transfer. The structure of the TMADH-ETF complex confirms the role of key residues in electron transfer and molecular assembly, originally suggested from detailed kinetic studies in wild-type and mutant complexes, and from molecular modelling.

Topics in Quaternion Linear Algebra

2014 ◽  
Author(s):  
Leiba Rodman
Keyword(s):  
Linear Algebra ◽  
Complex Analysis ◽  
Dimensional Space ◽  
Applied Mathematics ◽  
Three Dimensional ◽  
Number System ◽  
Graduate Course ◽  
Open Problems ◽  
Unpublished Research ◽  
Reference Tool

Quaternions are a number system that has become increasingly useful for representing the rotations of objects in three-dimensional space and has important applications in theoretical and applied mathematics, physics, computer science, and engineering. This is the first book to provide a systematic, accessible, and self-contained exposition of quaternion linear algebra. It features previously unpublished research results with complete proofs and many open problems at various levels, as well as more than 200 exercises to facilitate use by students and instructors. Applications presented in the book include numerical ranges, invariant semidefinite subspaces, differential equations with symmetries, and matrix equations. Designed for researchers and students across a variety of disciplines, the book can be read by anyone with a background in linear algebra, rudimentary complex analysis, and some multivariable calculus. Instructors will find it useful as a complementary text for undergraduate linear algebra courses or as a basis for a graduate course in linear algebra. The open problems can serve as research projects for undergraduates, topics for graduate students, or problems to be tackled by professional research mathematicians. The book is also an invaluable reference tool for researchers in fields where techniques based on quaternion analysis are used.

Extension of the Spatial PDI Model to Three Dimensions

1997 ◽  
Vol 84 (1) ◽  
pp. 176-178
Author(s):  
Frank O'Brien
Keyword(s):  
Population Density ◽  
Dimensional Space ◽  
Finite Lattice ◽  
Three Dimensional ◽  
Upper Bounds ◽  
Three Dimensions ◽  
Lower And Upper Bounds ◽  
Density Index ◽  
Three Dimensional Space

The author's population density index ( PDI) model is extended to three-dimensional distributions. A derived formula is presented that allows for the calculation of the lower and upper bounds of density in three-dimensional space for any finite lattice.

A Peptoid with Extended Shape in Water

2019 ◽  
Author(s):  
Jumpei Morimoto ◽  
Yasuhiro Fukuda ◽  
Takumu Watanabe ◽  
Daisuke Kuroda ◽  
Kouhei Tsumoto ◽  
...  
Keyword(s):  
Spectroscopic Analysis ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Biomolecular Recognition ◽  
Biological Application ◽  
New Class ◽  
Proteolytic Resistance ◽  
Pharmacokinetic Properties ◽  
Optically Pure ◽  
Three Dimensional Space

<div> <div> <div> <p>“Peptoids” was proposed, over decades ago, as a term describing analogs of peptides that exhibit better physicochemical and pharmacokinetic properties than peptides. Oligo-(N-substituted glycines) (oligo-NSG) was previously proposed as a peptoid due to its high proteolytic resistance and membrane permeability. However, oligo-NSG is conformationally flexible and is difficult to achieve a defined shape in water. This conformational flexibility is severely limiting biological application of oligo-NSG. Here, we propose oligo-(N-substituted alanines) (oligo-NSA) as a new peptoid that forms a defined shape in water. A synthetic method established in this study enabled the first isolation and conformational study of optically pure oligo-NSA. Computational simulations, crystallographic studies and spectroscopic analysis demonstrated the well-defined extended shape of oligo-NSA realized by backbone steric effects. The new class of peptoid achieves the constrained conformation without any assistance of N-substituents and serves as an ideal scaffold for displaying functional groups in well-defined three-dimensional space, which leads to effective biomolecular recognition. </p> </div> </div> </div>

Sign in / Sign up

Export Citation Format

Share Document