Chromatin: a tunable spring at work inside chromosomes

This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths, stretch modulus and twist-stretch coupling constant) of the so-called 30-nm chromatin fiber, in terms of DNA elastic properties and geometric properties of the fiber assembly. The computation naturally embeds the fiber within a current analytical model known as the ``extensible worm-like rope'', allowing a straightforward prediction of the force-extension curves. We show that these elastic constants are strongly sensitive to the linker length, up to 1 bp, or equivalently to its twist, and might locally reach very low values, yielding a highly flexible and extensible domain in the fiber. In particular, the twist-stretch coupling constant, reflecting the chirality of the chromatin fiber, exhibits steep variations and sign changes when the linker length is varied. We argue that this tunable elasticity might be a key feature for chromatin function, for instance in the initiation and regulation of transcription.Comment: 38 pages 15 figure

Hydro-Responsive Curling of the Resurrection Plant Selaginella lepidophylla

The spirally arranged stems of the spikemoss Selaginella lepidophylla, an ancient resurrection plant, compactly curl into a nest-ball shape upon dehydration. Due to its spiral phyllotaxy, older outer stems on the plant interlace and envelope the younger inner stems forming the plant centre. Stem curling is a morphological mechanism that limits photoinhibitory and thermal damages the plant might experience in arid environments. Here, we investigate the distinct conformational changes of outer and inner stems of S. lepidophylla triggered by dehydration. Outer stems bend into circular rings in a relatively short period of desiccation, whereas inner stems curl slowly into spirals due to hydro-actuated strain gradient along their length. This arrangement eases both the tight packing of the plant during desiccation and its fast opening upon rehydration. The insights gained from this work shed light on the hydro-responsive movements in plants and might contribute to the development of deployable structures with remarkable shape transformations in response to environmental stimuli

Conformation constraints for efficient viscoelastic fluid simulation

The simulation of high viscoelasticity poses important computational challenges. One is the difficulty to robustly measure strain and its derivatives in a medium without permanent structure. Another is the high stiffness of the governing differential equations. Solutions that tackle these challenges exist, but they are computationally slow. We propose a constraint-based model of viscoelasticity that enables efficient simulation of highly viscous and viscoelastic phenomena. Our model reformulates, in a constraint-based fashion, a constitutive model of viscoelasticity for polymeric fluids, which defines simple governing equations for a conformation tensor. The model can represent a diverse palette of materials, spanning elastoplastic, highly viscous, and inviscid liquid behaviors. In addition, we have designed a constrained dynamics solver that extends the position-based dynamics method to handle efficiently both position-based and velocity-based constraints. We show results that range from interactive simulation of viscoelastic effects to large-scale simulation of high viscosity with competitive performance

수동성 및 호혜성 한계를 극복하는 가변형 쌍이방성 음향 메타물질의 하향 설계

학위논문 (박사) -- 서울대학교 대학원 : 공과대학 전기·컴퓨터공학부, 2021. 2. 박남규.Over the past two decades, metamaterials have revolutionized how we manipulate classical waves. They allow us to obtain constitutive parameters beyond the bound of natural materials by artificially designing tailor-made resonance modes in the unit structure. Since all wave dynamics are anticipated from the constitutive parameters landscape in which the wave propagates, the implementation of entire constitutive parameters enables intriguing theoretical and practical applications in many wave systems, such as negative refraction and invisibility cloaking. Although various structures have been successfully proposed to obtain extraordinary wave properties, the design approach to the existing metamaterial poses fundamental challenges in realizing the physical properties. In many practical applications, metamaterial structures capable of independent control of each wave property has been envisaged as an ideal platform for reconfigurability. While metamaterial structures consisting of a combined substructure that controls one of the fundamental resonances have been proposed, it is required that an integrated platform offering decoupled control of the wave parameters. In particular, in the case of reconfigurable metamaterials, tuning the constitutive parameters depends on modifying the physical structure attached to the metamaterials, posing a fundamental challenge in the tuning range. Therefore, there is a need for a study to achieve flexible control and realize extreme properties. In this dissertation, I provide the top-down design approach of the reconfigurable acoustic metamaterial that overcomes conventional limitations and achieves designer wave properties. Based on the principles of decoupling of fundamental resonances, acoustic metamaterial platforms that offer independent control of wave parameters and their applications are presented. Then, I propose the concept of virtualized metamaterials on their signal response function to escape the boundary inherent in the physical structure of metamaterials, which generate artificial polarizations based on the digital signal processing technique, escaping physically resonating structure. Virtualized metamaterials enable decoupled control of all possible complex wave parameters in a reconfigurable manner and extreme wave properties. This dissertation is expected to provide a breakthrough in metamaterial design by implementing all wave properties independently, realizing designable frequency dispersion characteristics, and providing a flexible platform that can realize acoustic metamaterials' full capability.최근 20 년간 메타 물질은 파동제어 기법에 있어 혁신을 가져왔다. 메타물질은 단위 구조체에서의 공진 모드를 인공적으로 설계함으로써 자연 물질이 나타낼 수 없는 파동 물성의 구현을 가능케 한다. 모든 파동 현상은 파동이 전파되는 공간의 파동 물성 분포에 의해 결정되므로, 전자기파, 음파, 그리고 탄성파 등, 다양한 파동 영역에서 파동 물성의 완전한 제어는 음굴절, 클로킹과 같은 많은 흥미로운 현상을 가능하게 한다. 이와 같이 파동 물성의 극한적 제어를 위한 다양한 구조체가 제시되어 왔음에도 불구하고 기존의 메타 물질 설계 방식은 다음과 같은 근본적인 한계점을 갖는다. 대부분의 실용적인 목적의 메타 물질 응용을 위해서는 메타 물질의 재구성 가능성을 필요로 한다. 이를 위해 각 파동 물성에 대한 독립적인 제어가 가능한 구조체가 재구성 가능성에 적합한 구조로써 제시되어 왔으나, 파동 매개 변수의 분리가 가능한 대부분의 메타 물질은 하나의 기본 공진 모드를 제어하는 하위 구조의 조합으로 구성되므로, 하향식 제어를 제공하는 통합된 플랫폼에 대한 연구를 필요로 한다. 특히, 재구성 가능한 메타 물질의 경우 구성 매개 변수를 조정하는 능력은 메타 물질과 결합된 물리적 구조를 수정하는 능력에 따라 달라지므로, 실시간 동작에 있어 재구성 가능성에서 제어 가능한 영역의 범위에 근본적인 한계를 갖는다. 따라서 유연한 제어를 달성하고 극한 물성을 구현하기 위한 방법에 대한 연구가 필요하다. 본 학위 논문에서는 기존의 한계를 극복하고 결정론적으로 설계 가능한 파동 물성을 구현하기 위한 음향 메타 물질의 하향식 설계에 대해 분석한다. 기본 공진모드의 디커플링 원리를 기반으로, 파동 매개 변수를 독립적으로 제어 할 수 있는 음향 메타 물질 단위 구조체를 제안한다. 또한, 메타 물질의 물리적 구조에 의한 경계를 벗어나 디지털 신호 처리 기술을 기반으로 인공적인 분극을 구현하는 가상화 메타 물질의 개념을 제안한다. 가상화 메타 물질은 재구성 가능한 메타 물질로써, 가능한 모든 복소 파동 매개 변수를 분리 제어 할 수 있을 뿐만 아니라 극한 파동 물성을 구현할 수 있다. 본 연구는 모든 파동 물성을 독립적으로 구현할 뿐만 아니라, 설계 가능한 주파수 분산 특성을 실현함으로써 메타 물질 설계에 돌파구를 제공하고 음향 메타 물질의 전체 기능을 실현할 수 있는 유연한 플랫폼을 제공할 것으로 기대한다.Table of Contents Abstract i Table of Contents iv List of Figures viii Chapter 1. Introduction 1 1.1 Achievements and challenges in metamaterials 2 1.2 Outline of the dissertation 6 Chapter 2. Acoustic Wave Dynamics 8 2.1 Duality relation between acoustics and electromagnetics 9 2.2 Bianisotropy 12 2.2.1 Bianisotropy in electromagnetics 12 2.2.2 Acoustic bianisotropy 17 2.3 Experimental methods 20 Chapter 3. Top-down Design of Acoustic Metamaterials 22 3.1 Introduction to top-down approach to design metamaterials 23 3.2 Top-down design of bianisotropic acoustic metamaterials for underwater applications 26 3.3 Extended generalized Snell's law for independent manipulation of scattering wave-fronts 28 3.4 Space-coiling acoustic metamaterials for two-dimensional bianisotropic metamaterials 33 3.5 Conclusion 37 Chapter 4. Virtualized Metamaterials 38 4.1 Introduction to the concept of virtualized metamaterials 39 4.2 Digitally virtualized acoustic metamaterials 41 4.2.1 Virtualization of the signal response of meta-atom 41 4.2.2 On-demand tuning of dispersion 50 4.2.3 Independent control of monopolar and dipolar scattering 53 4.2.4 Transient response of the virtual metamaterial 58 4.3 Experimental setup 62 4.4 Conclusion 63 Chapter 5. Extreme Acoustic Properties beyond Passivity and Reciprocity Bounds 65 5.1 Introduction to limit of bianisotropic media 66 5.2 Extreme acoustic properties 67 5.2.1 Bianisotropy beyond the passivity bound 67 5.2.2 Extreme nonreciprocity 73 5.2.3 Broadband-, flat-frequency dispersion 81 5.3 Experimental setup 85 5.4 Conclusion 86 Chapter 6. Conclusion 87 Appendix A. Supplements for Chapter 4 89 A.1 Monopolar and dipolar model of the virtualized atom 89 A.2 Power gain of active metamaterials 93 A.3 Effective medium parameters and impedance matching 94 Appendix B. Supplements for Chapter 5 101 B.1 Polarizability and scattering matrix 101 B.2 Derivation of the maximum Willis coupling in a one-dimensional passive system 105 B.3 Scattering matrix in the virtual meta-atom structure 108 B.4 Causality conditions of the frequency dispersion 111 Bibliography 113 Abstract in Korean 123Docto

Wearable performance

This is the post-print version of the article. The official published version can be accessed from the link below - Copyright @ 2009 Taylor & FrancisWearable computing devices worn on the body provide the potential for digital interaction in the world. A new stage of computing technology at the beginning of the 21st Century links the personal and the pervasive through mobile wearables. The convergence between the miniaturisation of microchips (nanotechnology), intelligent textile or interfacial materials production, advances in biotechnology and the growth of wireless, ubiquitous computing emphasises not only mobility but integration into clothing or the human body. In artistic contexts one expects such integrated wearable devices to have the two-way function of interface instruments (e.g. sensor data acquisition and exchange) worn for particular purposes, either for communication with the environment or various aesthetic and compositional expressions. 'Wearable performance' briefly surveys the context for wearables in the performance arts and distinguishes display and performative/interfacial garments. It then focuses on the authors' experiments with 'design in motion' and digital performance, examining prototyping at the DAP-Lab which involves transdisciplinary convergences between fashion and dance, interactive system architecture, electronic textiles, wearable technologies and digital animation. The concept of an 'evolving' garment design that is materialised (mobilised) in live performance between partners originates from DAP Lab's work with telepresence and distributed media addressing the 'connective tissues' and 'wearabilities' of projected bodies through a study of shared embodiment and perception/proprioception in the wearer (tactile sensory processing). Such notions of wearability are applied both to the immediate sensory processing on the performer's body and to the processing of the responsive, animate environment. Wearable computing devices worn on the body provide the potential for digital interaction in the world. A new stage of computing technology at the beginning of the 21st Century links the personal and the pervasive through mobile wearables. The convergence between the miniaturisation of microchips (nanotechnology), intelligent textile or interfacial materials production, advances in biotechnology and the growth of wireless, ubiquitous computing emphasises not only mobility but integration into clothing or the human body. In artistic contexts one expects such integrated wearable devices to have the two-way function of interface instruments (e.g. sensor data acquisition and exchange) worn for particular purposes, either for communication with the environment or various aesthetic and compositional expressions. 'Wearable performance' briefly surveys the context for wearables in the performance arts and distinguishes display and performative/interfacial garments. It then focuses on the authors' experiments with 'design in motion' and digital performance, examining prototyping at the DAP-Lab which involves transdisciplinary convergences between fashion and dance, interactive system architecture, electronic textiles, wearable technologies and digital animation. The concept of an 'evolving' garment design that is materialised (mobilised) in live performance between partners originates from DAP Lab's work with telepresence and distributed media addressing the 'connective tissues' and 'wearabilities' of projected bodies through a study of shared embodiment and perception/proprioception in the wearer (tactile sensory processing). Such notions of wearability are applied both to the immediate sensory processing on the performer's body and to the processing of the responsive, animate environment