Group-theoretic analysis of symmetry-preserving deployable structures and metamaterials.

Many deployable structures in nature, as well as human-made mechanisms, preserve symmetry as their configurations evolve. Examples in nature include blooming flowers, dilation of the iris within the human eye, viral capsid maturation and molecular and bacterial motors. Engineered examples include opening umbrellas, elongating scissor jacks, variable apertures in cameras, expanding Hoberman spheres and some kinds of morphing origami structures.

Rate of Entropy Production in Stochastic Mechanical Systems.

Entropy production in stochastic mechanical systems is examined here with strict bounds on its rate. Stochastic mechanical systems include pure diffusions in Euclidean space or on Lie groups, as well as systems evolving on phase space for which the fluctuation-dissipation theorem applies, i.e.

A Mosquito Pick-and-Place System for PfSPZ-based Malaria Vaccine Production.

Unlabelled: The treatment of malaria is a global health challenge that stands to benefit from the widespread introduction of a vaccine for the disease. A method has been developed to create a live organism vaccine using the sporozoites (SPZ) of the parasite (Pf), which are concentrated in the salivary glands of infected mosquitoes. Current manual dissection methods to obtain these PfSPZ are not optimally efficient for large-scale vaccine production.

Continuous body 3-D reconstruction of limbless animals.

Limbless animals such as snakes, limbless lizards, worms, eels and lampreys move their slender, long bodies in three dimensions to traverse diverse environments. Accurately quantifying their continuous body's 3-D shape and motion is important for understanding body-environment interactions in complex terrain, but this is difficult to achieve (especially for local orientation and rotation). Here, we describe an interpolation method to quantify continuous body 3-D position and orientation.

Black-Scholes Theory and Diffusion Processes on the Cotangent Bundle of the Affine Group.

The Black-Scholes partial differential equation (PDE) from mathematical finance has been analysed extensively and it is well known that the equation can be reduced to a heat equation on Euclidean space by a logarithmic transformation of variables. However, an alternative interpretation is proposed in this paper by reframing the PDE as evolving on a Lie group. This equation can be transformed into a diffusion process and solved using mean and covariance propagation techniques developed previously in the context of solving Fokker-Planck equations on Lie groups.

Lateral Oscillation and Body Compliance Help Snakes and Snake Robots Stably Traverse Large, Smooth Obstacles.

Snakes can move through almost any terrain. Similarly, snake robots hold the promise as a versatile platform to traverse complex environments such as earthquake rubble. Unlike snake locomotion on flat surfaces which is inherently stable, when snakes traverse complex terrain by deforming their body out of plane, it becomes challenging to maintain stability.

Mathematical aspects of molecular replacement. V. Isolating feasible regions in motion spaces.

This paper mathematically characterizes the tiny feasible regions within the vast 6D rotation-translation space in a full molecular replacement (MR) search. The capability to a priori isolate such regions is potentially important for enhancing robustness and efficiency in computational phasing in macromolecular crystallography (MX). The previous four papers in this series have concentrated on the properties of the full configuration space of rigid bodies that move relative to each other with crystallographic symmetry constraints.

Quantizing Euclidean Motions via Double-Coset Decomposition.

Concepts from mathematical crystallography and group theory are used here to quantize the group of rigid-body motions, resulting in a "motion alphabet" with which robot motion primitives are expressed. From these primitives it is possible to develop a dictionary of physical actions. Equipped with an alphabet of the sort developed here, intelligent actions of robots in the world can be approximated with finite sequences of characters, thereby forming the foundation of a language in which robot motion is articulated.

Phantom with multiple active points for ultrasound calibration.

Accurate tracking and localization of ultrasound (US) images are used in various computer-assisted interventions. US calibration is a preoperative procedure to recover the transformation bridging the tracking sensor and the US image coordinate systems. Although many calibration phantom designs have been proposed, a limitation that hinders the resulted calibration accuracy is US elevational beam thickness.

Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures.

Assessing preferred relative rigid body position and orientation is important in the description of biomolecular structures (such as proteins) and their interactions. In this article, we extend and apply the "symmetrical parameterization," which we recently introduced in the kinematics community, to address problems in structural biology. We also review parameterization methods that are widely used in structural biology to describe relative rigid body motions (in particular, orientations) as a basis for comparison.

Mathematical aspects of molecular replacement. IV. Measure-theoretic decompositions of motion spaces.

In molecular-replacement (MR) searches, spaces of motions are explored for determining the appropriate placement of rigid-body models of macromolecules in crystallographic asymmetric units. The properties of the space of non-redundant motions in an MR search, called a `motion space', are the subject of this series of papers. This paper, the fourth in the series, builds on the others by showing that when the space group of a macromolecular crystal can be decomposed into a product of two space subgroups that share only the lattice translation group, the decomposition of the group provides different decompositions of the corresponding motion spaces.

Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy.

Cryo-electron microscopy (EM) and small angle X-ray scattering (SAXS) are two different data acquisition modalities often used to glean information about the structure of large biomolecular complexes in their native states. A SAXS experiment is generally considered fast and easy but unveils the structure at very low resolution, whereas a cryo-EM experiment needs more extensive preparation and postacquisition computation to yield a three-dimensional (3D) density map at higher resolution. In certain applications, we may need to verify whether the data acquired in the SAXS and cryo-EM experiments correspond to the same structure (e.

Computational Analysis of SAXS Data Acquisition.

Small-angle x-ray scattering (SAXS) is an experimental biophysical method used for gaining insight into the structure of large biomolecular complexes. Under appropriate chemical conditions, the information obtained from a SAXS experiment can be equated to the pair distribution function, which is the distribution of distances between every pair of points in the complex. Here we develop a mathematical model to calculate the pair distribution function for a structure of known density, and analyze the computational complexity of these calculations.

Framed curves and knotted DNA.

The present mini-review covers the local and global geometry of framed curves and the computation of twist and writhe in knotted DNA circles. Classical inequalities relating the total amount of bending of a closed space curve and associated knot parameters are also explained.

Multiscale modeling of double-helical DNA and RNA: a unification through Lie groups.

Several different mechanical models of double-helical nucleic-acid structures that have been presented in the literature are reviewed here together with a new analysis method that provides a reconciliation between these disparate models. In all cases, terminology and basic results from the theory of Lie groups are used to describe rigid-body motions in a coordinate-free way, and when necessary, coordinates are introduced in a way in which simple equations result. We consider double-helical DNAs and RNAs which, in their unstressed referential state, have backbones that are either straight, slightly precurved, or bent by the action of a protein or other bound molecule.

Mathematical aspects of molecular replacement. II. Geometry of motion spaces.

Molecular replacement (MR) is a well established computational method for phasing in macromolecular crystallography. In MR searches, spaces of motions are explored for determining the appropriate placement of rigid models of macromolecules in crystallographic asymmetric units. In the first paper of this series, it was shown that this space of motions, when endowed with an appropriate composition operator, forms an algebraic structure called a quasigroup.

Mathematical aspects of molecular replacement. I. Algebraic properties of motion spaces.

Molecular replacement (MR) is a well established method for phasing of X-ray diffraction patterns for crystals composed of biological macromolecules of known chemical structure but unknown conformation. In MR, the starting point is known structural domains that are presumed to be similar in shape to those in the macromolecular structure which is to be determined. A search is then performed over positions and orientations of the known domains within a model of the crystallographic asymmetric unit so as to best match a computed diffraction pattern with experimental data.

A Stochastic Kinematic Model of Class Averaging in Single-Particle Electron Microscopy.

Single-particle electron microscopy is an experimental technique that is used to determine the 3D structure of biological macromolecules and the complexes that they form. In general, image processing techniques and reconstruction algorithms are applied to micrographs, which are two-dimensional (2D) images taken by electron microscopes. Each of these planar images can be thought of as a projection of the macromolecular structure of interest from an a priori unknown direction.

Modeling loop entropy.

Proteins fold from a highly disordered state into a highly ordered one. Traditionally, the folding problem has been stated as one of predicting "the" tertiary structure from sequential information. However, new evidence suggests that the ensemble of unfolded forms may not be as disordered as once believed, and that the native form of many proteins may not be described by a single conformation, but rather an ensemble of its own.

The Path-of-Probability Algorithm for Steering and Feedback Control of Flexible Needles.

In this paper we develop a new framework for path planning of flexible needles with bevel tips. Based on a stochastic model of needle steering, the probability density function for the needle tip pose is approximated as a Gaussian. The means and covariances are estimated using an error propagation algorithm which has second order accuracy.

INFORMATION-THEORETIC INEQUALITIES ON UNIMODULAR LIE GROUPS.

Classical inequalities used in information theory such as those of de Bruijn, Fisher, Cramér, Rao, and Kullback carry over in a natural way from Euclidean space to unimodular Lie groups. These are groups that possess an integration measure that is simultaneously invariant under left and right shifts. All commutative groups are unimodular.

Position and Orientation Distributions for Non-Reversal Random Walks using Space-Group Fourier Transforms.

This paper presents an efficient group-theoretic approach for computing the statistics of non-reversal random walks (NRRW) on lattices. These framed walks evolve on proper crystallographic space groups. In a previous paper we introduced a convolution method for computing the statistics of NRRWs in which the convolution product is defined relative to the space-group operation.

Group theory and biomolecular conformation: I. Mathematical and computational models.

Biological macromolecules, and the complexes that they form, can be described in a variety of ways ranging from quantum mechanical and atomic chemical models, to coarser grained models of secondary structure and domains, to continuum models. At each of these levels, group theory can be used to describe both geometric symmetries and conformational motion. In this survey, a detailed account is provided of how group theory has been applied across computational structural biology to analyze the conformational shape and motion of macromolecules and complexes.

Equilibrium Conformations of Concentric-tube Continuum Robots.

Robots consisting of several concentric, preshaped, elastic tubes can work dexterously in narrow, constrained, and/or winding spaces, as are commonly found in minimally invasive surgery. Previous models of these "active cannulas" assume piecewise constant precurvature of component tubes and neglect torsion in curved sections of the device. In this paper we develop a new coordinate-free energy formulation that accounts for general preshaping of an arbitrary number of component tubes, and which explicitly includes both bending and torsion throughout the device.

Deblurring of Class-Averaged Images in Single-Particle Electron Microscopy.

This paper proposes a method for deblurring of class-averaged images in single-particle electron microscopy (EM). Since EM images of biological samples are very noisy, the images which are nominally identical projection images are often grouped, aligned and averaged in order to cancel or reduce the background noise. However, the noise in the individual EM images generates errors in the alignment process, which creates an inherent limit on the accuracy of the resulting class averages.