Our research group uses computational methods to provide fundamental, molecular-level understanding of biological and material systems, with the aim of discovering new phenomena and developing new materials and technologies. The methods we use or develop are largely based on statistical mechanics, molecular modeling and simulations, stochastic dynamics, coarse-graining, bioinformatics, machine learning, and polymer/colloidal physics. Our current research interests fall within four main themes:
  1. Genome organization and regulation
  2. Polymer-nanoparticle composites
  3. Viral-DNA-packaging molecular motors
  4. DNA-based nanomachines
Below we describe brief descriptions of the specific research projects in the group. Further details may be obtained from individual publications.

Genome organization and regulation
In eukayotic organisms, DNA is organized into repeating units called nucleosomes, each of which consist of ~1.65 turns of DNA wrapped around an octamer of histone proteins. The array of nucleosomes is folded into a thicker chromatin fiber that undergoes further looping to eventually yield chromosomes. Our group is interested in developing novel computational methods to elucidate this 3D organization of DNA and its role in biological processes like transcription. Our earliest efforts involved the development of a state-of-the-art mesoscopic model of nucleosome arrays (Fig. 1) and a tailored Monte Carlo approach for simulating conformations of the arrays. Our modeling provided the first evidence of the chromatin fiber exhibiting a polymorphic structure, displaying a mixture of zigzag and solenoidal conformations; These results were verified by a EM-assisted nucleosome interaction capture experiments from the S. Grigoryev lab. The model also importantly allowed us to dissect the roles of the linker histone, salt condition, and the four types of histone tails in chromatin folding.

Figure 1

Figure 2

More recently, we have used these models to investigate the effects of torsional stresses on chromatin. DNA is subjected to myriad torsional stresses in vivo, which until now were viewed as a byproduct of biological processes that needed to be eliminated by specialized enzymes. However, new evidence suggests that torsional stresses serve important roles in gene regulation, but little is known about how these stresses propagate within chromatin and affect its organization. Our work now provides the first detailed picture of the structure and dynamics of torsionally stressed chromatin and revealed a new mechanism, nucleosome phasing, by which the torsional response of chromatin could be modulated. In related work, we have mapped out the free energy landscape of mononucleosomes (Fig. 2) and nucleosome arrays to investigate differences in the conformational fluctuations of nucleosomes in isolation and those present within arrays.
Another focus is on developing methods to elucidate the 3D organization of chromatin within chromosomal domains. We have developed a novel strategy for recovering ensembles of chromatin conformations from contact probabilities (CPs) between genomic loci, as measured from chromosome conformation capture experiments. Our approach involves iterative adjustment of parameters of a polymer model of chromatin via an adaptive filter approach until the CPs estimated from simulations of the model match those obtained experimentally (Fig. 3). To speed up ensemble recovery, we devised a new method for estimating CPs based on functional approximations of inter-bed distance distributions obtained from polymer simulations. We are currently using these methods to investigate structural changes in specific loci in association with B-cell development and cancer therapy, in collaboration with Dr. C. Murre and Dr. M. G. Rosenfeld. Concurrently, we are developing software that will allow researchers to obtain enzyme cleavage fractions in their Hi-C experiments and obtain CP maps with much higher resolution than afforded by current methods.

Figure 3

Nanoparticle-polymer composites
The incorporation of nanoparticles into polymers constitutes a powerful strategy for introducing new optical, electrical, and magnetic functionalities into the polymers and for enhancing their mechanical properties. We are working on many different aspects of nanoparticle-polymer composites. Our main focus is on understanding how shaped, polymer-grafted nanoparticles interact with each other and how one could manipulate such interactions to make the particles assemble into higher-order structures relevant to plasmonic, photovoltaic, and shock mitigation applications. A key feature of this work is the use of advanced Monte Carlo methods to compute free energies and phase diagrams relevant to assembly. Our efforts have led to a remarkably simple strategy, involving changes in the length of grafted chains, for tuning the interparticle orientation of silver nanocubes between face-to-face and edge-to-edge configurations (Fig. 4) that has been experimentally demonstrated by the group of Dr. Andrea Tao.

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The ability to characterize higher-order structures formed by nanoparticle assembly is critical for predicting and engineering the properties of advanced nanocomposite materials. We are developing an automated quantitative image analysis tool that will allow researchers to analyze electron microscopy images of nanocomposites and obtain a range of structural properties of nanoparticle clusters as they assemble into higher-order structures (Fig. 5). The first version of this software, named particle image characterization tool or PICT, is coded in MATLAB R2012b and is available for download from the MATLAB Exchange Server. To gain further insights into the assembly mechanism, we have developed a computational approach that will allow researchers to recover key dynamic parameters of nanoparticle assembly from the analysis of static, disjointed microscopy images of nanoparticle composites.
In another project, in collaboration with the groups of Dr. Sia Nemat-Nasser and Dr. Zhibin Guan, we are developing new and improved elastomeric composite materials for mitigating and/or redirecting blast-induced stress waves over a range of frequencies and energies. Our group is using a range of computational methods to provide molecular-level insights into energy dissipation and redirection within polymer nanocomposites as a function of polymer architecture and nanoparticle composition. Some of our ongoing work includes developing high-resolution coarse-grained models of polyurea, the polymer currently used for the above application, and examining its viscoelastic properties and shock response (Fig. 6) using equilibrium and nonequilibrium molecular dynamics simulations to dissect the molecular origins of its superior dissipative properties. In a related project, we are collaborating with Dr. Darren Lipomi to develop molecular design rules for the design of bulk heterojunctions for photovoltaics with superior mechanical and electronic properties.

Figure 6

Viral DNA packaging motors
We have recently become interested in how viruses package their genomes into capsids. In particular, many DNA viruses utilize a powerful molecular motor during assembly to translocate DNA into a preformed capsid shell. Our collaborator, Dr. Douglas Smith, has used elegant single-molecule experiments with optical traps (Fig. 7) to show that these motors are capable of generating forces in excess of 60 pN and packaging DNA at rates of 200 to 2000 bp/s, making them the most powerful molecular motor known to mankind. The molecular mechanisms by which these motors generate such large forces and high packaging speeds remain largely unknown. Our lab is using a range of computational tools, in combination with experiments in the Smith lab, to resolve these mechanisms. Uncovering such mechanisms would not resolve a fundamental problem in virology but also provide insights into combating viral infections like herpes and designing synthetic mimics of these powerful molecular motors.

Figure 7

Figure 8

We started by investigating the DNA packaging mechanism of the T4 bacteriophage motor by carrying out single-molecule DNA packaging measurements and free energy calculations via the MM-GBSA approach. In particular, we tested a previously proposed mechanism of packaging in which the T4 motor protein translocates DNA by transitioning between an extended and a compact state due to electrostatic interactions between complimentarily charged residues across an interface between two domains of the motor (Fig. 7). We showed that site-directed alterations in these residues cause force dependent impairments of motor function that correlate well with computed changes in free-energy differences between the two states, thus providing support for the proposed model. We also proposed an energy landscape model of motor activity under external loads that couples the free-energy profile of motor conformational states with that of the ATP hydrolysis cycle (Fig. 8).
In a subsequent study, we carried out free energy decomposition analysis to identify key molecular interactions and residues involved in force generation (Fig. 9). We found that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identified specific charged and uncharged residues, and the specific interactions that these residues mediate, at the interface that play a dominant role in the compaction transition. The computed contributions were found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. We are currently examining other aspects of packaging, including the 3D arrangement of the subunits comprising the T4 motor and the conformational relaxation of DNA within the capsids.

Figure 9

DNA-based nanomachines
DNA nanotechnology holds great promise for creating mechanically dynamic and functional nanomachines with many potential applications. We have recently embarked on a new project on the design of DNA-based nanostructures capable of actuated mechanical motion, in collaboration with Dr. Carlos Castro. Our lab is developing software tools that will allow researchers to build 3D atomistic models of DNA-origami structure designs. We are also developing protocols for simulating the dynamics of these DNA nanostructures, which will then be used for optimizing the design parameters. One of first DNA nanostructures that we have studied is the DNA "hinge" designed and synthesized by the Carlos lab (Fig. 10), whereby the angle subtended by the hinge arms can be tuned by varying the length of the single-stranded DNA connection. At the same time, we are developing statistical mechanical models to investigate salt-dependent actuation of hinge arms.

Figure 10