Evolution of adaptive force chains in reconfigurable granular metamaterials.

Under an externally applied load, granular packings form force chains that depend on the contact network and moduli of the grains. In this work, we investigate packings of variable modulus (VM) particles, where we can direct force chains by changing the Young's modulus of individual particles within the packing on demand. Each VM particle is made of a silicone shell that encapsulates a core made of a low-melting-point metallic alloy (Field's metal).

Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure in vivo.

Correction: Flow and clogging of capillary droplets.

Correction for 'Flow and clogging of capillary droplets' by Yuxuan Cheng , , 2024, https://doi.org/10.1039/D4SM00752B.

Flow and clogging of capillary droplets.

Capillary droplets form due to surface tension when two immiscible fluids are mixed. We describe the motion of gravity-driven capillary droplets flowing through narrow constrictions and obstacle arrays in both simulations and experiments. Our new capillary deformable particle model recapitulates the shape and velocity of single oil droplets in water as they pass through narrow constrictions in microfluidic chambers.

Identifying topologically associating domains using differential kernels.

Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional (3D) structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture techniques generate Hi-C maps that can provide insight into the 3D structure of chromatin.

Computational modeling of the physical features that influence breast cancer invasion into adipose tissue.

Breast cancer invasion into adipose tissue strongly influences disease progression and metastasis. The degree of cancer cell invasion into adipose tissue depends on both biochemical signaling and the mechanical properties of cancer cells, adipocytes, and other key components of adipose tissue. We model breast cancer invasion into adipose tissue using discrete element method simulations of active, cohesive spherical particles (cancer cells) invading into confluent packings of deformable polyhedra (adipocytes).

Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.

Proteins naturally occur in crowded cellular environments and interact with other proteins, nucleic acids, and organelles. Since most previous experimental protein structure determination techniques require that proteins occur in idealized, non-physiological environments, the effects of realistic cellular environments on protein structure are largely unexplored. Recently, Förster resonance energy transfer (FRET) has been shown to be an effective experimental method for investigating protein structure .

Protein folding as a jamming transition.

Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of found in experimental measurements. We show that as the hydrophobic interactions increase relative to the temperature, a novel jamming transition occurs when the core packing fraction exceeds .

Connecting polymer collapse and the onset of jamming.

Previous studies have shown that the interiors of proteins are densely packed, reaching packing fractions that are as large as those found for static packings of individual amino-acid-shaped particles. How can the interiors of proteins take on such high packing fractions given that amino acids are connected by peptide bonds and many amino acids are hydrophobic with attractive interactions? We investigate this question by comparing the structural and mechanical properties of collapsed attractive disk-shaped bead-spring polymers to those of three reference systems: static packings of repulsive disks, of attractive disks, and of repulsive disk-shaped bead-spring polymers. We show that the attractive systems quenched to temperatures below the glass transition T≪T_{g} and static packings of both repulsive disks and bead-spring polymers possess similar interior packing fractions.

Computational modeling of the physical features that influence breast cancer invasion into adipose tissue.

Breast cancer invasion into adipose tissue strongly influences disease progression and metastasis. The degree of cancer cell invasion into adipose tissue depends on numerous biochemical and physical properties of cancer cells, adipocytes, and other key components of adipose tissue. We model breast cancer invasion into adipose tissue as a physical process by carrying out simulations of active, cohesive spherical particles (cancer cells) invading into confluent packings of deformable polyhedra (adipocytes).

Modeling the Effects of Varying the Ti Concentration on the Mechanical Properties of Cu-Ti Alloys.

The mechanical properties of CuTi alloys have been characterized extensively through experimental studies. However, a detailed understanding of why the strength of Cu increases after a small fraction of Ti atoms are added to the alloy is still missing. In this work, we address this question using density functional theory (DFT) and molecular dynamics (MD) simulations with the modified embedded atom method (MEAM) interatomic potentials.

How cells with diverse stator composition collectively swarm.

Swarming is a macroscopic phenomenon in which surface bacteria organize into a motile population. The flagellar motor that drives swarming in is powered by stators MotAB and MotCD. Deletion of the MotCD stator eliminates swarming, whereas deletion of the MotAB stator enhances swarming.

Designing the pressure-dependent shear modulus using tessellated granular metamaterials.

Jammed packings of granular materials display complex mechanical response. For example, the ensemble-averaged shear modulus 〈G〉 increases as a power law in pressure p for static packings of soft spherical particles that can rearrange during compression. We seek to design granular materials with shear moduli that can either increase or decrease with pressure without particle rearrangements even in the large-system limit.

Local and global measures of the shear moduli of jammed disk packings.

Strain-controlled isotropic compression gives rise to jammed packings of repulsive, frictionless disks with either positive or negative global shear moduli. We carry out computational studies to understand the contributions of the negative shear moduli to the mechanical response of jammed disk packings. We first decompose the ensemble-averaged, global shear modulus as 〈G〉=(1-F_{-})〈G_{+}〉+F_{-}〈G_{-}〉, where F_{-} is the fraction of jammed packings with negative shear moduli and 〈G_{+}〉 and 〈G_{-}〉 are the average values from packings with positive and negative moduli, respectively.

How individual cells with diverse stator distributions collectively form a heterogeneous macroscopic swarming population.

Unlabelled: Swarming is a macroscopic phenomenon in which surface bacteria organize into a motile population. The flagellar motor that drives swarming in is powered by stators MotAB and MotCD. Deletion of the MotCD stator eliminates swarming, whereas deletion of the MotAB stator enhances swarming.

Localized growth and remodelling drives spongy mesophyll morphogenesis.

The spongy mesophyll is a complex, porous tissue found in plant leaves that enables carbon capture and provides mechanical stability. Unlike many other biological tissues, which remain confluent throughout development, the spongy mesophyll must develop from an initially confluent tissue into a tortuous network of cells with a large proportion of intercellular airspace. How the airspace in the spongy mesophyll develops while the tissue remains mechanically stable is unknown.

Hopper flows of deformable particles.

Numerous experimental and computational studies show that continuous hopper flows of granular materials obey the Beverloo equation that relates the volume flow rate and the orifice width : ∼ (/ - ), where is the average particle diameter, is an offset where ∼ 0, the power-law scaling exponent = - 1/2, and is the spatial dimension. Recent studies of hopper flows of deformable particles in different background fluids suggest that the particle stiffness and dissipation mechanism can also strongly affect the power-law scaling exponent . We carry out computational studies of hopper flows of deformable particles with both kinetic friction and background fluid dissipation in two and three dimensions.

Core packing of well-defined X-ray and NMR structures is the same.

Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by X-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints.

Correction: The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions.

Correction for 'The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions' by Dong Wang , , 2021, , 9901-9915, DOI: 10.1039/D1SM01228B.

The structural, vibrational, and mechanical properties of jammed packings of deformable particles in three dimensions.

We investigate the structural, vibrational, and mechanical properties of jammed packings of deformable particles with shape degrees of freedom in three dimensions (3D). Each 3D deformable particle is modeled as a surface-triangulated polyhedron, with spherical vertices whose positions are determined by a shape-energy function with terms that constrain the particle surface area, volume, and curvature, and prevent interparticle overlap. We show that jammed packings of deformable particles without bending energy possess low-frequency, quartic vibrational modes, whose number decreases with increasing asphericity and matches the number of missing contacts relative to the isostatic value.

Using delaunay triangularization to characterize non-affine displacement fields during athermal, quasistatic deformation of amorphous solids.

We investigate the non-affine displacement fields that occur in two-dimensional Lennard-Jones models of metallic glasses subjected to athermal, quasistatic simple shear (AQS). During AQS, the shear stress strain displays continuous quasi-elastic segments punctuated by rapid drops in shear stress, which correspond to atomic rearrangement events. We capture all information concerning the atomic motion during the quasi-elastic segments and shear stress drops by performing Delaunay triangularizations and tracking the deformation gradient tensor associated with each triangle .

Mechanical response of packings of nonspherical particles: A case study of two-dimensional packings of circulo-lines.

We investigate the mechanical response of jammed packings of circulo-lines in two spatial dimensions, interacting via purely repulsive, linear spring forces, as a function of pressure P during athermal, quasistatic isotropic compression. The surface of a circulo-line is defined as the collection of points that is equidistant to a line; circulo-lines are composed of a rectangular central shaft with two semicircular end caps. Prior work has shown that the ensemble-averaged shear modulus for jammed disk packings scales as a power law, 〈G(P)〉∼P^{β}, with β∼0.

Static-state particle fabrication via rapid vitrification of a thixotropic medium.

Functional particles that respond to external stimuli are spurring technological evolution across various disciplines. While large-scale production of functional particles is needed for their use in real-life applications, precise control over particle shapes and directional properties has remained elusive for high-throughput processes. We developed a high-throughput emulsion-based process that exploits rapid vitrification of a thixotropic medium to manufacture diverse functional particles in large quantities.