MPM based simulation for various solid deformation

Solid materials are responsible for many interesting phenomena. There are various types of them such as deformable objects and granular materials. In this paper, we present an MPM based framework to simulate the wide range of solid materials. In this framework, solid mechanics is based on the elastoplastic model, where we use von Mises criterion for deformable objects, and the Drucker-Prager model with non-associated plastic flow rules for granular materials. As a result, we can simulate different kinds of deformation of deformable objects and sloping failure for granular materials

Lagrangian Neural Style Transfer for Fluids

Artistically controlling the shape, motion and appearance of fluid simulations pose major challenges in visual effects production. In this paper, we present a neural style transfer approach from images to 3D fluids formulated in a Lagrangian viewpoint. Using particles for style transfer has unique benefits compared to grid-based techniques. Attributes are stored on the particles and hence are trivially transported by the particle motion. This intrinsically ensures temporal consistency of the optimized stylized structure and notably improves the resulting quality. Simultaneously, the expensive, recursive alignment of stylization velocity fields of grid approaches is unnecessary, reducing the computation time to less than an hour and rendering neural flow stylization practical in production settings. Moreover, the Lagrangian representation improves artistic control as it allows for multi-fluid stylization and consistent color transfer from images, and the generality of the method enables stylization of smoke and liquids likewise.Comment: ACM Transaction on Graphics (SIGGRAPH 2020), additional materials: http://www.byungsoo.me/project/lnst/index.htm

Integrating Peridynamics with Material Point Method for Elastoplastic Material Modeling

© Springer Nature Switzerland AG 2019. We present a novel integral-based Material Point Method (MPM) using state based peridynamics structure for modeling elastoplastic material and fracture animation. Previous partial derivative based MPM studies face challenges of underlying instability issues of particle distribution and the complexity of modeling discontinuities. To alleviate these problems, we integrate the strain metric in the basic elastic constitutive model by using material point truss structure, which outweighs differential-based methods in both accuracy and stability. To model plasticity, we incorporate our constitutive model with deviatoric flow theory and a simple yield function. It is straightforward to handle the problem of cracking in our hybrid framework. Our method adopts two time integration ways to update crack interface and fracture inner parts, which overcome the unnecessary grid duplication. Our work can create a wide range of material phenomenon including elasticity, plasticity, and fracture. Our framework provides an attractive method for producing elastoplastic materials and fracture with visual realism and high stability

The Regioselective Conjugation of the 15-nt Thrombin Aptamer with an Optimized Tripeptide Sequence Greatly Increases the Anticoagulant Activity of the Aptamer

Currently, oligonucleotide therapy has emerged as a new paradigm in the treatment of human diseases. In many cases, however, therapeutic oligonucleotides cannot be used directly without modification. Chemical modification or the conjugation of therapeutic oligonucleotides is required to increase their stability or specificity, improve their affinity or inhibitory characteristics, and address delivery issues. Recently, we proposed a conjugation strategy for a 15-nt G-quadruplex thrombin aptamer aimed at extending the recognition interface of the aptamer. In particular, we have prepared a series of designer peptide conjugates of the thrombin aptamer, showing improved anticoagulant activity. Herein, we report a new series of aptamer–peptide conjugates with optimized peptide sequences. The anti-thrombotic activity of aptamer conjugates was notably improved. The lead conjugate, TBA–GLE, was able to inhibit thrombin-induced coagulation approximately six-fold more efficiently than the unmodified aptamer. In terms of its anticoagulant activity, the TBA–GLE conjugate approaches NU172, one of the most potent G-quadruplex thrombin aptamers. Molecular dynamics studies have confirmed that the principles applied to the design of the peptide side chain are efficient instruments for improving aptamer characteristics for the proposed TBA conjugate model

Quantification of target proteins using hydrogel antibody arrays and MALDI time-of-flight mass spectrometry (A2M2S)

Mass spectrometry-based analysis techniques are widely applied in proteomics. This study presents a novel method for quantitative multiplex candidate protein profiling. It applies immunocapture of differentially labeled protein complements on hydrogel antibody arrays and subsequent quantification by MS. To make this approach quantitative a labeling approach was devised. The impact of labeling on the antibody/antigen interaction was assessed in detail by surface plasmon resonance. Owing to the resolution by mass more than two protein samples can be compared simultaneously. Direct labeling of crude samples such as sera was developed and so enables the absolute quantification of target proteins straight from crude samples without a protein purification step. It was used to measure the concentration of apolipoprotein A-1 in serum. This method has been termed A2M2S for Affinity Arrays and MALDI Mass Spectrometry

Anticoagulant Oligonucleotide–Peptide Conjugates: Identification of Thrombin Aptamer Conjugates with Improved Characteristics

Oligonucleotide–peptide conjugates (OPCs) are a promising class of biologically active compounds with proven potential for improving nucleic acid therapeutics. OPCs are commonly recognized as an efficient instrument to enhance the cellular delivery of therapeutic nucleic acids. In addition to this application field, OPCs have an as yet unexplored potential for the post-SELEX optimization of DNA aptamers. In this paper, we report the preparation of designer thrombin aptamer OPCs with peptide side chains anchored to a particular thymidine residue of the aptamer. The current conjugation strategy utilizes unmodified short peptides and support-bound protected oligonucleotides with activated carboxyl functionality at the T3 thymine nucleobase. The respective modification of the oligonucleotide strand was implemented using N3-derivatized thymidine phosphoramidite. Aptamer OPCs retained the G-quadruplex architecture of the parent DNA structure and showed minor to moderate stabilization. In a series of five OPCs, conjugates bearing T3–Ser–Phe–Asn (SFN) or T3–Tyr–Trp–Asn (YWN) side chains exhibited considerably improved anticoagulant characteristics. Molecular dynamics studies of the aptamer OPC complexes with thrombin revealed the roles of the amino acid nature and sequence in the peptide subunit in modulating the anticoagulant activity