576 research outputs found
Nonlinear torsional analysis of 3D composite beams using the extended St. Venant solution
No full textWe present in this paper a finite element formulation for nonlinear torsional analysis of 3D beams with arbitrary composite cross-sections. Since the proposed formulation employs a continuum mechanics based beam element with kinematics enriched by the extended St. Venant solutions, it can precisely account higher order warping effect and its 3D couplings. We propose a numerical procedure to calculate the extended St. Venant equation and the twisting center of an arbitrary composite cross-section simultaneously. The accuracy and efficiency of the proposed formulation are thoroughly investigated through representative numerical examples.
Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
Get PDFDNA nanotechnology enables the programmed synthesis of intricate nanometer-scale structures for diverse applications in materials and biological science. Precise control over the 3D solution shape and mechanical flexibility of target designs is important to achieve desired functionality. Because experimental validation of designed nanostructures is time-consuming and cost-intensive, predictive physical models of nanostructure shape and flexibility have the capacity to enhance dramatically the design process. Here, we significantly extend and experimentally validate a computational modeling framework for DNA origami previously presented as CanDo [Castro,C.E., Kilchherr,F., Kim,D.-N., Shiao,E.L., Wauer,T., Wortmann,P., Bathe,M., Dietz,H. (2011) A primer to scaffolded DNA origami. Nat. Meth., 8, 221–229.]. 3D solution shape and flexibility are predicted from basepair connectivity maps now accounting for nicks in the DNA double helix, entropic elasticity of single-stranded DNA, and distant crossovers required to model wireframe structures, in addition to previous modeling (Castro,C.E., et al.) that accounted only for the canonical twist, bend and stretch stiffness of double-helical DNA domains. Systematic experimental validation of nanostructure flexibility mediated by internal crossover density probed using a 32-helix DNA bundle demonstrates for the first time that our model not only predicts the 3D solution shape of complex DNA nanostructures but also their mechanical flexibility. Thus, our model represents an important advance in the quantitative understanding of DNA-based nanostructure shape and flexibility, and we anticipate that this model will increase significantly the number and variety of synthetic nanostructures designed using nucleic acids.MIT Faculty Start-up Fun
A general model reduction with primal assembly in structural dynamics
No full textA new formulation of general model reduction in structural dynamics is presented. The proposed method consists of four attributes: a hybrid method combining dynamic condensation and component mode synthesis that are arguably the most popular model reduction techniques, a precise model reduction taking the inertia effect into consideration, primal assembly at the boundary interface of substructures and general formulations of model reduction with primal assembly. Comparisons of the proposed model reduction method with the conventional methods are provided as well as an efficient model reduction procedure of the proposed method. In particular, its advantages and performance of the proposed method are thoroughly investigated with various numerical examples. (C) 2017 Elsevier B.V. All rights reserved.OAIID:RECH_ACHV_DSTSH_NO:T201722255RECH_ACHV_FG:RR00200001ADJUST_YN:EMP_ID:A080440CITE_RATE:4.441FILENAME:A general model reduction with primal assembly in structural dynamics.pdfDEPT_NM:바이오시스템·소재학부EMAIL:[email protected]_YN:YFILEURL:https://srnd.snu.ac.kr/eXrepEIR/fws/file/2e081a5a-c096-49e7-9cc6-8520272619dd/linkN
Conformational dynamics of supramolecular protein assemblies
Get PDFSupramolecular protein assemblies including molecular motors, cytoskeletal filaments, chaperones, and ribosomes play a central role in a broad array of cellular functions ranging from cell division and motility to RNA and protein synthesis and folding. Single-particle reconstructions of such assemblies have been growing rapidly in recent years, providing increasingly high resolution structural information under native conditions. While the static structure of these assemblies provides essential insight into their mechanism of biological function, their dynamical motions provide additional important information that cannot be inferred from structure alone. Here we present an unsupervised computational framework for the analysis of high molecular weight protein assemblies and use it to analyze the conformational dynamics of structures deposited in the Electron Microscopy Data Bank. Protein assemblies are modeled using a recently introduced coarse-grained modeling framework based on the finite element method, which is used to compute equilibrium thermal fluctuations, elastic strain energy distributions associated with specific conformational transitions, and dynamical correlations in distant molecular domains. Results are presented in detail for the ribosome-bound termination factor RF2 from Escherichia coli, the nuclear pore complex from Dictyostelium discoideum, and the chaperonin GroEL from E. coli. Elastic strain energy distributions reveal hinge-regions associated with specific conformational change pathways, and correlations in collective molecular motions reveal dynamical coupling between distant molecular domains that suggest new, as well as confirm existing, allosteric mechanisms. Results are publically available for use in further investigation and interpretation of biological function including cooperative transitions, allosteric communication, and molecular mechanics, as well as in further classification and refinement of electron microscopy based structures.Massachusetts Institute of Technology (MIT Faculty Start-up Funds)Massachusetts Institute of Technology (Samuel A. Goldblith Career Development Professorship
Precise and selective macroscopic assembly of a dual lock-and-key structured hydrogel
No full textMacroscopic assembly offers immense potential for constructing complex systems due to the high design flexibility of the building blocks. In such assembly systems, hydrogels are promising candidates for building blocks due to their versatile chemical compositions and ease of property tuning. However, two major challenges must be addressed to facilitate application in a broader context: the precision of assembly and the quantity of orthogonally matching pairs must both be increased. Although previous studies have attempted to address these challenges, none have successfully dealt with both simultaneously. Here, we propose topology-based design criteria for the selective assembly of hydrogel building blocks. By introducing the dual lock-and-key structures, we demonstrate highly precise assembly exclusively between the matching pairs. We establish principles for selecting multiple orthogonally matching pairs and achieve selective assembly involving simple one-to-one matching and complex assemblies with multiple orthogonal matching points. Moreover, by harnessing hydrogel tunability and the abundance of matching pairs, we synthesize complementary single-stranded structures for programmable assembly and successfully assemble them in the correct order. Finally, we demonstrate a hydrogel-based self-assembled logic gate system, including a YES gate, an OR gate, and an AND gate. The output is generated only when the corresponding inputs are provided according to each logic. In this work, we introduce dual lock-and-key structures for highly selective and precise macroscopic assembly of hydrogel building blocks. This work demonstrates diverse assembly ranging from simple to complex structures.
Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy
No full textTwo-dimensional (2D) DNA origami that is capable of self-assembling into complex 2D and 3D geometries pave the way for a bottom-up synthesis for various applications in nano/biotechnology. Here, we directly visualized the aqueous structure of 2D DNA origami cross-tiles and their assemblies using cryogenic electron microscopy. We uncovered flexible arms in cross-tile monomers and designated inter-tile folding. In addition, we observed the formation of clusters and stacks of DNA cross-tiles in solution, which could potentially affect the interaction and assembly of DNA origami. Finally, we quantitatively evaluated the flexibility of DNA origami in solution using finite element analysis. Our discovery has laid the foundation for investigating the dynamic structures of 2D DNA origami assemblies in solution, providing insights regarding the self-assembly and self-replication mechanisms of 2D DNA origami
Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies
No full textThe conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function
Contributions to the anisotropic elasto-plastic analysis of shells
Get PDFThesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 2009.Includes bibliographical references (p. 133-142).Shells are probably the most widely used structural component in engineering and also in nature due to their high efficiency and excellent performance when properly designed. On the other hand, they can be very sensitive to changes in geometries, thicknesses, applied loads and boundary conditions. Hence much research effort has been devoted to the reliable and efficient analysis of shells. This work contributes to the anisotropic elasto-plastic analysis of shells by addressing key issues in developing shell elements for finite element analysis and an elasto-plasticity model considering anisotropy and its evolution. First we develop a shell element that models the three-dimensional (3D) effects of surface tractions. The element is the widely used MITC4 shell element enriched by the use of a fully 3D stress-strain description, appropriate through-the-thickness displacements to model surface tractions, and pressure degrees of freedom for incompressible analyses. The element formulation avoids instabilities and ill-conditioning. We also develop a triangular 6-node shell element that represents an important improvement over a recently published element. The element is spatially isotropic, passes the membrane and bending patch tests, contains no spurious zero energy mode, and is formulated without an artificial constant. In particular, the improved element does not show the instability sometimes observed with the earlier published element.(cont.) Finally we review a constitutive model for anisotropic elasto-plastic analysis which takes into account the anisotropy of both the elastic and plastic material behaviors, as well as their evolution with plastic strains. It is based on continuum energy considerations, the Lee decomposition of deformations and a stored energy function of the logarithmic strains. The present work focuses on giving some physical insight into the parameters of the model and their effects on the predictions in proportional and in non-proportional loading conditions.by Do-Nyun Kim.Ph.D
The intergenerational transmission of maternal adverse childhood experiences on offsprings psychiatric disorder and the mediating role of maternal depression: Results from a cross sectional study
No full text© The Author(s) 2022.Maternal adverse childhood experiences (ACEs) may negatively affect the mental health and development of their offspring. The purpose of this study was to investigate the association of maternal ACE and offsprings psychiatric disorder and the mediating effect of maternal depression. The subjects included 463 mothers (42.78 ± 5.68 years) and their offspring aged 6–18 years (13.26 ± 3.90 years). Mothers reported their ACE before age 18 and completed the Beck Depression Inventory-II and Diagnostic Predictive Scales (DPS), a screening tool for offsprings psychiatric disorder. 35.42% of subjects had at least one ACE, and 11.0% reported three or more ACEs. Higher maternal ACE scores were associated with a significantly higher prevalence of offsprings psychiatric disorders (p < 0.001). Household dysfunction of maternal ACE (OR = 2.263, p < 0.001) is significantly associated with offsprings psychiatric disorder. In the mediation model in which the household dysfunction affects the number of offsprings psychiatric disorders, the partial mediation model through maternal depression was significant. The mothers experience of household dysfunction before the age of 18 has a significant impact on her offsprings psychiatric disorder and supported significant mediation through maternal depression. Further research is needed to determine the mechanisms of intergenerational transmission of ACE and offsprings psychopathology.N
Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards
No full textWe employ the single-particle fluorescence nanoscopy technique points accumulation for imaging in nanoscale topography (PAINT) using site-specific DNA probes to acquire two-dimensional density maps of specific features patterned on nanoscale DNA origami pegboards. We show that PAINT has a localization accuracy of ∼10 nm that is sufficient to reliably distinguish dense (>10[superscript 4] features μm[superscript –2]) sub-100 nm patterns of oligonucleotide features. We employ two-color PAINT to follow enzyme-catalyzed modification of features on individual origami and to show that single nanopegboards exhibit stable, spatially heterogeneous probe-binding patterns, or “fingerprints.” Finally, we present experimental and modeling evidence suggesting that these fingerprints may arise from feature spacing variations that locally modulate the probe binding kinetics. Our study highlights the power of fluorescence nanoscopy to perform quality control on individual soft nanodevices that interact with and position reagents in solution.National Science Foundation (U.S.) (Collaborative Research Award CCF-0829579)United States. Multidisciplinary University Research Initiative (W911NF-12-1-0420
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