Faculty Research

Photo of Monica Olvera de la Cruz

Monica Olvera de la Cruz

  • Elastic Shells
  • Elastic Driven Self Assembly
  • Electrostatics at Liquid Interfaces
  • Ionic Gels
  • Co-assembly of Biological and Synthetic Molecules
  • Statistics, Thermodynamics and Dynamics of Complex Molecular Fluids
  • Atomistic Modeling

Olvera de la Cruz Research Highlights

Strong Attractions and Repulsions Mediated by Monovalent Salts
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Facilitated Dissociation of Transciption Factors from Single DNA Binding Sites
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Effective Interactions between Spherical Nucleic Acid-Au Nanoparticles
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Aggregation of Heterogeneously Charged Colloids 
  
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Emergent Perversions in the Buckling of Heterogeneous Elastic Strips
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Electrstatics-Driven Hierarchcial Buckling of Charged Flexible Ribbons

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Michael Bedzyk

  • Semiconductor and metal-oxide surface structures
  • Liquid/solid interface
  • X-ray probes for Ultra-thin-films and Nanostructures
  • Nanoscale Structures
  • In Situ X-ray Synchrotron
  • Molecular self assembly

Bedzyk Research Highlights

Eletrolyte-Mediated Assembly of Charged Nanoparticles
Highlights                                     Paper

Photo of Erik Luijten

Erik Luijten

  • Colloidal systems
  • Electrostatically driven self-assembly
  • Algorithm development
  • Polymeric materials

Luijten Research Highlights:

Computational Soft Matter Lab
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Photo of Mani  Madhav

Mani Madhav

  • Model-driven measurement of forces in living epithelia
  • Mechanical-feedback in morphogenesis
  • Spatially patterned differentiation
  • Transcriptional-advection and morphogenesis

Madhav Research Highlights:

General Research Interests
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Photo of John Marko

John Marko

  • The application of statistical mechanics and polymer physics to biophysical problems
  • Micromechanical studies of DNA, DNA-protein interactions, and chromosome structure
  • Experimental and theoretical research
Photo of Mark Ratner

Mark Ratner

  • Electron transfer, electron transport, and electron dynamics
  • Molecular assemblies, packing, and interactions
  • Quantum dynamics, and its relation to environmental baths and decoherence
  • Organic devices, both single molecule and adlayer-based
  • Energy applications of several sorts
Photo of George  Schatz

George Schatz

  • Optical properties of nanoparticles and nanoparticle arrays and aggregates
  • DNA structure, thermodynamics and dynamics
  • Self assembly of soft materials
  • Mechanical properties of nanomaterials
  • Exciton formation, relaxation and thermal transport
Photo of David  Schwab

David Schwab

Photo of Sam  Stupp

Sam Stupp

  • Self-Assembly
  • Energy Materials 
  • Biomaterials
Photo of igal  Szleifer

igal Szleifer

  • Biophysics of Lipids
  • Biologically Inspired Nanomaterials
  • Responsive Polymer Layers
Photo of Danielle Tullman-Ercek

Danielle Tullman-Ercek

CCTSM Catalyst Award Recipient
  • Determining rules for protein shell assembly
  • Engineering protein shells for new geometries and functions
  • Controlling transport across biological membranes
  • Scaffolding inorganic nanostructures on biological templates
  • Producing protein biomaterials with designed properties


Student Research

Photo of Shuangping  Liu

Shuangping Liu

Fourth-year Ph.D. student in the Department of Materials Science and Engineering

Shuangping Liu Research Interests

Emergent perversions in the buckling of heterogeneous elastic strips Highlight

Perversions in an otherwise uniform helical structure provide the mechanism of helical symmetry breaking. In this work, using a three-dimensional elastomeric bistrip model, we investigate the intrinsic properties of perversions that are independent of specific strip shapes. Besides the fundamental role as generic domain walls that connect states of distinct symmetries, this study reveals richer physics of perversions in the threedimensional elastic system. The major findings include the condensation of strain energy over perversions, the identification of the repulsive nature of the perversion-perversion interaction, and the
coalescence of perversions. These intrinsic properties of perversions may have implications to the understanding of relevant biological motifs and the designing of micro-muscles and soft robotics.
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HETEROGENEOUS NANO-GEL ELASTICITY

In Prof. Olvera de la Cruz’s group he works on determining the dynamics of heterogeneous nano-gel elasticity. Gels can undergo large deformations in response to the external stimuli, including temperature, pH, and electric field, which has generated increasing interest for diverse technological applications. The heterogeneous nature of gels and the interplay of the stress field with various environmental fields can lead to very complex mechanical instabilities like creases and buckles which cannot be fully captured by pure theoretical analysis. Within the framework of finite element method, the main aim of Shuangping’s research is to numerically model, tune and predict the properties and behavior of gels as well as other soft materials by connecting the principle of mechanics, electrostatics and thermodynamics to both the experiments and the molecular-level simulations.

Photo of Kurinji  Krishnamoorthy

Kurinji Krishnamoorthy

4th Year Ph.D. Student in Department of Applied Physics
Email Kurinji

In Prof. Michael Bedzyk Group she works to develop new types of in situ X-ray scattering experiments that will discover the underling structure of the building blocks that lead to this assembly. Watson-Crick hybridization is the short-range interaction that most of the attention has gone to, but this competes against the longer-range electrostatic forces set up by the highly negatively charges DNA screened by the surrounding ionic solution. This electrostatic interaction is the focus of Kurinji’s research. Her experiments focus on this interaction by designing DNA-coated nanoparticles that disallow Watson-Crick hybridization. She then uses in situ small-angle X-ray scattering (SAXS) at the Advanced Photon Source (APS) to follow the structural changes in the counter ion cloud surrounding the spherical nucleic acid (SNA) nanoparticles as a function of bulk ionic conditions and length and duplexing of nucleic acid chains. A major part of her experimental work is to develop analysis methods that derive structural properties that are directly comparable to theoretical computational models.

Photo of Lam-Kiu Fong

Lam-Kiu Fong

4th year Ph.D. student, Department of Chemistry
Email Lam-Kiu

In Prof. George Schatz and Prof. Chad Mirken, she works on DNA-functionalized gold nanoparticles (DNA-AuNPs) experimentally exhibit an enhanced binding affinity for complementary DNA, compared to free DNA systems.Understanding this effect is important for the design of DNA-AuNPs for diagnostic and therapeutic applications, because their mechanism of action depends on the energetics of duplex hybridization onto the surface. Though the enhancement in binding affinity is thought to be a result of the high local DNA density on the nanoparticle surface, a mechanistic description of this phenomenon is lacking. All-atom, explicit solvent simulations provide the most realistic description of DNA structure and dynamics, but the time scales necessary to capture DNA melting have previously been computationally prohibitive for systems of this size and complexity. We use atomistic molecular dynamics simulations to quantify the effect of DNA surface density on the melting mechanism of a DNA duplex that is chemically bonded to a surface. From these simulations we gain insight into how three local environmental variables affect the mechanism of DNA duplex melting and contribute to an increased hybridization energy. First, we investigate how steric encumbrance resulting from the dense arrangement of other DNA strands on the nanoparticle surface increase duplex hybridization enthalpy due to unfavorable electrostatics. Second, we consider that due to this dense DNA arrangement, the duplex resides in an electrostatically complex environment resulting from the polyanionic nature of DNA and the high local counter ion concentration. Third, we explore how the proximity of neighboring strands to the duplex creates an enhanced local concentration of binding sites, which has been credited as the main driving force behind the binding enhancement. By using a quantitative DNA forcefield we aim to describe the contribution these have on DNA hybridization with three systems of increasing complexity: 1) a DNA 9-mer duplex free in solution; 2) a DNA 9-mer duplex attached to a gold surface; and 3) a DNA 9-mer duplex attached to a densely DNA-functionalized gold surface. We determine duplex stability during melting for each system and describe the molecular effects of closely packed neighboring DNA strands on hybridization energy. With a fundamental understanding of this melting mechanism we will develop a set of guidelines delineating what structural parameters most contribute to the energetics of DNA-AuNP-based therapeutics and diagnostics.

Photo of Huanxin  Wu

Huanxin Wu

Fourth-year Ph.D. student in the Department of Physics & Astronomy

DIELECTRIC EFFECTS IN SOFT MATTER SYSTEMS


In Prof. Erik Luijten’s group, his work focuses on dielectric effects in various soft-matter systems. Electrostatic interactions are ubiquitous and of fundamental importance for understanding many physical and biological systems, including colloidal suspensions, membranes and the redox process at mineral-solution interfaces. Although continuum models are widely used, they are only accurate in limited parameter regimes, as the polarization and many-body effects are often ignored. This is mainly due to the formidable computational challenge to solve the Poisson equation with dielectric mismatch at material interfaces dynamically for each simulation step. A boundary–element method (BEM) based algorithm for sharp dielectric interfaces was recently implemented and optimized for mobile dielectrics in our group. The main goal of Huanxin’s research is to extend the current BEM dielectric algorithm to volume elements for bulk dielectrics while maintaining the efficiency gained by the GMRES and fast Ewald solver.  This will not only help us to understand dielectric effects at a more accurate level but also enables us to look at soft-matter systems that have never been fully resolved before. Huanxin also makes extensions and improvements to the dielectric algorithm in the group.

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Rebecca Menssen

Second-year Ph.D. student in the Department of Engineering Science and Applied Mathematics

DNA DYNAMICS AND GENE EXPRESSION REGULATION

In Prof. Madhav Mani’s group her work is focused on understanding how the mechanics and information contained within the DNA of complex organisms, couples together to regulate gene expression during organismal development and homeostasis. A novel experiment by the Gregor Lab at Princeton has provided the first dynamic insight into this process in Drosophilia embryos. Importantly, this experiment highlights the 3-dimensional location of transcriptionally active loci in real-time, as well as a direct and quantitative readout of its activity (number of currently loaded polymerase). Unlike studying an analogous system in the dish, we have access to the dynamics within a very precise developmental context where the level of gene activity is carefully modulated along the head-tail axis of the y. More importantly, the extremely precise nature of gene activity in the y permits comparison across embryos, which allows statistically meaningful measurements to be made. The main aim of Rebecca’s research is to use this experimental system to develop, a) an image and data analysis toolbox that allows statistically meaningful, and physically-motivated, measurements of this beautiful coupling between information and mechanics, and b) the hand-in-hand construction of a model/theory that demonstrates how the DNA is packaged and the nature of the statistical polymer mechanics of gene regulation. This model/theory can be developed from analyzing the data to look for patterns or unique behavior.

Photo of Ha-Kyung Kwon

Ha-Kyung Kwon

Fourth-year Ph.D. student in the Department of Material Science and Engineering

Determining the Phase Behavior of Ion-containing Polymers

In Profesor Olvera de la Cruz's group Ha-Kyung works on determining the phase behavior of ion-containing polymers. Recent developments in high-density energy storage devices have heightened the search for materials that are mechanically robust and highly tunable. Polyelectrolyte blends and copolymers, consisting of at least one charged species, are ideal candidate materials for fuel cell and battery membranes, as they combine the mechanical stability of the polymer chain with the ion-selective conductivity of the charged backbone. Specifically, using charged constituents in a copolymer has been shown to be a powerful way to control the self-assembled nanostructures in the copolymer by introducing local ionic correlations between the charged backbone and the counterions. It has been recently shown that local ionic correlations, incorporated via liquid state (LS) theory, enhance phase separation of the copolymer even in the absence of polymer interactions, leading to nanostructures that are highly desirable for transport but inaccessible in neutral block copolymers. The goal of Ha-Kyung's research is to investigate the influence of ionic correlations on the phase diagram of polyelectrolyte blends and charged-neutral block copolymers using a combination of hybrid theories and experiments, with the goal of being able to elucidate the effects of electrostatic interactions on the bulk phase behavior of polymeric systems and the role of salt at the interfaces of these polymeric materials. 

Alumni Research

Photo of Yufei Jing

Yufei Jing

Ph.D., Applied Physics

Charged Interfaces

Yufei was a member of Professor Olvera de la Cruz's group and worked on determining the dynamics of heterogeneous nano-gel elasticity. Gels can undergo large deformations in response to the external stimuli, including temperature, pH, and electric field, which has generated increasing interest for diverse technological applications.  The heterogeneous nature of gels and the interplay of the atress field with various environmental fields can lead to very complex mechanical instabilities like creases and buckles which can not be fully captured by pure theoretical analysis.  Within the framework of finite element method, the main aim of Shuangping's research is to numberically model, tune and predict the properties and behavior of gels as well as other soft materials by connecting the principle of mechanics, electrostatics and thermodynamics to both the experiments and the molecular-level simulations.

Yufei Jing Research Interests