Engineering topics

de la Cruz, Monica Olvera

Publications and source records attributed to de la Cruz, Monica Olvera.

11 records

DOE OSTI2024

Heterogeneous flexibility can contribute to chromatin segregation in the cell nucleus

The highly and slightly condensed forms of chromatin, heterochromatin and euchromatin, respectively, segregate in the cell nucleus. Heterochromatin is more abundant in the nucleus periphery. Here, in this work, we study the mechanism of heterochromatin segregation by modeling interphase chromosomes as diblock ring copolymers confined in a rigid spherical shell using molecular dynamics simulations. In our model, heterochromatin and euchromatin are distinguished by their bending stiffnesses only, while an interaction potential between the spherical shell and chromatin is used to model lamin-associated proteins. Our simulations indicate that in the absence of attractive interactions between the nuclear shell and the chromatin, most heterochromatin segregates towards the nuclear interior due to the depletion of less flexible heterochromatin segments from the nuclear periphery. This inverted chromatin distribution, which is opposite to the conventional case with heterochromatin dominating at the periphery, is in accord with experimental observations in rod cells. This “inversion” is also found to be independent of the heterochromatin concentration and chromosome number. The chromatin distribution at the periphery found in vivo can be recovered by further increasing the bending stiffness of heterochromatin segments or by turning on attractive interactions between the nuclear shell and heterochromatin. Our results indicate that the bending stiffness of chromatin could be a contributor to chromosome organization along with differential effects of HP ⁢1⁢𝛼-driven phase segregation and of loop extruders and interactions with the nuclear envelope and topological constraints.

biomolecular & subcellular processes↗

DOE OSTI2023

Molecular entrapment via homopolymer self-assembly

The present invention provides novel nanostructures comprising solution of PPSU 20 . Methods of preparing the novel PPSU nanostructures, and applications of such nanostructures are also provided.

Scott, Evan A.↗

DOE OSTI2023

Colloidal Clusters and Networks Formed by Oppositely Charged Nanoparticles with Varying Stiffnesses

Colloidal clusters and gels are ubiquitous in science and technology. Particle softness has a strong effect on interparticle interactions; however, our understanding of the role of this factor in the formation of colloidal clusters and gels is only beginning to evolve. Here, we report the results of experimental and simulation studies of the impact of particle softness on the assembly of clusters and networks from mixtures of oppositely charged polymer nanoparticles (NPs). Experiments were performed below or above the polymer glass transition temperature, at which the interaction potential and adhesive forces between the NPs were significantly varied. Hard NPs assembled in fractal clusters that subsequently organized in a kinetically arrested colloidal gel, while soft NPs formed dense precipitating aggregates, due to the NP deformation and the decreased interparticle distance. Importantly, interactions of hard and soft NPs led to the formation of discrete precipitating NP aggregates at a relatively low volume fraction of soft NPs. A phenomenological model was developed for interactions of oppositely charged NPs with varying softnesses. Furthermore, the experimental results were in agreement with molecular dynamics simulations based on the model. This work provides insight on interparticle interactions before, during, and after the formation of hard–hard, hard–soft, and soft–soft contacts and has impact for numerous applications of reversible colloidal gels, including their use as inks for additive manufacturing.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

DOE OSTI2022

Microporous water with high gas solubilities

Liquids with permanent microporosity can absorb larger quantities of gas molecules than conventional solvents , providing new opportunities for liquid-phase gas storage, transport, and reactivity. Current approaches to designing porous liquids rely on sterically bulky solvent molecules or surface ligands and thus are not amenable to many important solvents, including water. Here, we report a generalizable thermodynamic strategy to preserve permanent microporosity and impart high gas solubilities to liquid water. Specifically, we show how the external and internal surface chemistry of microporous zeolite and metal–organic framework nanocrystals can be tailored to promote the formation of stable dispersions in water while maintaining dry networks of micropores that are accessible to gas molecules. As a result of their permanent microporosity, these aqueous fluids can concentrate gases, including oxygen (O 2 ) and carbon dioxide (CO 2 ), to much higher densities than are found in typical aqueous environments. Furthermore, when these fluids are oxygenated, record-high capacities of O 2 can be delivered to hypoxic red blood cells, highlighting one potential application of this new class of microporous liquids for physiological gas transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Specific Ion Effects in Lanthanide–Amphiphile Structures at the Air–Water Interface and Their Implications for Selective Separation

The use of surfactants to attract dissolved ions to water surfaces and interfaces is an essential step in both solvent-based and solvent-free separation processes. Here, we have studied the interactions of lanthanide ions in the aqueous subphase with monolayers of dihexadecyl phosphate at air–water interfaces. With heavier lanthanides (atomic number Z ≥ 65) in the subphase, the floating layer can be compressed to an area/molecule of about half the molecular cross section, indicating bilayer formation. X-ray fluorescence and reflectivity data support this conclusion. In the presence of lighter lanthanides (Z < 65), only monolayers are observed. Subphase-concentration-dependent studies using Er 3+ (heavier) and Nd 3+ (lighter) lanthanides show a stepwise progression, with ions attaching to the monolayer only when the solution concentration is >3 × 10 –7 M. Above ~10 –5 M, bilayers form but only in the presence of the heavier lanthanide. Grazing incidence X-ray diffraction shows evidence of lateral ion–ion correlations in the bilayer structure but not in monolayers. Explicit solvent all-atom molecular dynamics simulations confirm the elevated ion–ion correlation in the bilayer system. This bilayer structure isolates heavier lanthanides but not lighter lanthanides from an aqueous solution and is therefore a potential mechanism for the selective separation of heavier lanthanides.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Polar state reversal in active fluids

Spontaneous emergence of correlated states such as flocks and vortices is a prime example of collective dynamics and self-organization observed in active matter. In geometrically confined systems, the formation of globally correlated polar states proceeds through the emergence of a macroscopic steadily rotating vortex, which spontaneously selects a clockwise or counterclockwise global chiral state. In this work, we reveal that a global vortex formed by colloidal rollers exhibits polar state reversal and that a subsequent formation of the collective states upon re-energizing the system is not random. We combine experiments and simulations to elucidate how a combination of hydrodynamic and electrostatic interactions leads to hidden asymmetries in the local particle positional order, reflecting the chiral state of the system. These asymmetries can be exploited to systematically command subsequent polar states of active liquids through temporal control of the activity.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2021

Origin of Proteolytic Stability of Peptide-Brush Polymers as Globular Proteomimetics

Peptide-brush polymers (PBPs), wherein every side-chain of the polymers is peptidic, represent a new class of proteomimetic with unusually high proteolytic resistance while maintaining bioactivity. Here, we sought to determine the origin of this behavior and to assess its generality via a combined theory and experimental approach. A series of PBPs with various polymer backbone structures were prepared and examined for their proteolytic stability and bioactivity. We discovered that an increase in the hydrophobicity of the polymer backbones is predictive of an elevation in proteolytic stability of the side-chain peptides. Computer simulations, together with small-angle X-ray scattering (SAXS) analysis, revealed globular morphologies for these polymers, in which pendant peptides condense around hydrophobic synthetic polymer backbones driven by the hydrophobic effect. As the hydrophobicity of the polymer backbones increases, the extent of solvent exposure of peptide cleavage sites decreases, reducing their accessibility to proteolytic enzymes. This study provides insight into the important factors driving PBP aqueous-phase structures to behave as globular, synthetic polymer-based proteomimetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Quincke Oscillations of Colloids at Planar Electrodes

Dielectric particles in weakly conducting fluids rotate spontaneously when subject to strong electric fields. Such Quincke rotation near a plane electrode leads to particle translation that enables physical models of active matter. In this Letter, we show that Quincke rollers can also exhibit oscillatory dynamics, whereby particles move back and forth about a fixed location. We explain how oscillations arise for micron-scale particles commensurate with the thickness of a field-induced boundary layer in the nonpolar electrolyte. This work enables the design of colloidal oscillators.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Hoobas: A highly object-oriented builder for molecular dynamics

Polydispersity and random sequences are ubiquitous features of polymers, and molecular dynamics simulations can help elucidate the impact of disorder in polymer systems. However, currently available packages for building polymer topologies do not enable the user to include randomness in a straightforward fashion. Here, we introduce Hoobas, a molecular builder package that easily handles polydispersity using a prototype-builder design pattern. This enables fast and easy building of systems comprised of thousands of distinct objects. It is written in the Python programming language, which ensures compatibility with a wide range of molecular dynamics packages and tools, as well as easy integration into most workflows.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Fast and programmable locomotion of hydrogel-metal hybrids under light and magnetic fields

The design of soft matter in which internal fuels or an external energy input can generate locomotion and shape transformations observed in living organisms is a key challenge. Such materials could assist in productive functions that may range from robotics to smart management of chemical reactions and communication with cells. In this context, hydrated matter that can function in aqueous media would be of great interest. Here, we report the design of hydrogels containing a scaffold of high–aspect ratio ferromagnetic nanowires with nematic order dispersed in a polymer network that change shape in response to light and experience torques in rotating magnetic fields. The synergistic response enables fast walking motion of macroscopic objects in water on either flat or inclined surfaces and also guides delivery of cargo through rolling motion and light-driven shape changes. The theoretical description of the response to the external energy input allowed us to program specific trajectories of hydrogel objects that were verified experimentally.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Homopolymer self-assembly of poly(propylene sulfone) hydrogels via dynamic noncovalent sulfone-sulfone bonding

Natural biomolecules such as peptides and DNA can dynamically self-organize into diverse hierarchical structures. Mimicry of this homopolymer self-assembly using synthetic systems has remained limited but would be advantageous for the design of adaptive bio/nanomaterials. Here, we report both experiments and simulations on the dynamic network self-assembly and subsequent collapse of the synthetic homopolymer poly(propylene sulfone). The assembly is directed by dynamic noncovalent sulfone–sulfone bonds that are susceptible to solvent polarity. The hydration history, specified by the stepwise increase in water ratio within lower polarity water-miscible solvents like dimethylsulfoxide, controls the homopolymer assembly into crystalline frameworks or uniform nanostructured hydrogels of spherical, vesicular, or cylindrical morphologies. These electrostatic hydrogels have a high affinity for a wide range of organic solutes, achieving >95% encapsulation efficiency for hydrophilic small molecules and biologics. This system validates sulfone–sulfone bonding for dynamic self-assembly, presenting a robust platform for controllable gelation, nanofabrication, and molecular encapsulation.

59 BASIC BIOLOGICAL SCIENCES↗