Super-Resolution Genome Mapping in Silicon Nanochannels.

Optical genome mapping in nanochannels is a powerful genetic analysis method, complementary to deoxyribonucleic acid (DNA) sequencing. The method is based on detecting a pattern of fluorescent labels attached along individual DNA molecules. When such molecules are extended in nanochannels, the labels create a fluorescent genetic barcode that is used for mapping the DNA molecule to its genomic locus and identifying large-scale variation from the genome reference.

Buckling of an elastic rod embedded on an elastomeric matrix: planar vs. non-planar configurations.

We investigate the buckling of a slender rod embedded in a soft elastomeric matrix through a combination of experiments, numerics and theory. Depending on the control parameters, both planar wavy (2D) or non-planar coiled (3D) configurations are observed in the post-buckling regime. Our analytical and numerical results indicate that the rod buckles into 2D configurations when the compression forces associated to the two lowest critical modes are well separated.

Structural transition from helices to hemihelices.

Helices are amongst the most common structures in nature and in some cases, such as tethered plant tendrils, a more complex but related shape, the hemihelix forms. In its simplest form it consists of two helices of opposite chirality joined by a perversion. A recent, simple experiment using elastomer strips reveals that hemihelices with multiple reversals of chirality can also occur, a richness not anticipated by existing analyses.

Differential contributions of conformation extension and domain unfolding to properties of fibronectin nanotextiles.

Fibronectin (FN) textiles are built as nanometer-thick fabrics. When uniaxially loaded, these fabrics exhibit a distinct threshold between elastic and plastic deformation with increasing stretch. Fabric mechanics are modeled using an eight-chain network and two-state model, revealing that elastic properties of FN depend on conformational extension of the protein and that plastic deformation depends on domain unfolding.

Fluctuating elastic filaments under distributed loads.

Filaments under distributed loads are common in biological systems. In this paper, we study the thermo-mechanical properties of an extensible thermally fluctuating elastic filament under distributed forces. The ground state of the filament is solved first, followed by an investigation of the thermal fluctuations around the ground state.

Entropically driven motion of polymers in nonuniform nanochannels.

In nanofluidic devices, nonuniform confinement induces an entropic force that automatically drives biopolymers toward less-confined regions to gain entropy. To understand this phenomenon, we first analyze the diffusion of an entropy-driven particle system. The derived Fokker-Planck equation reveals an effective driving force as the negative gradient of the free energy.

Transition between two regimes describing internal fluctuation of DNA in a nanochannel.

We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime.

Mechanics of forced unfolding of proteins.

We describe and solve a two-state kinetic model for the forced unfolding of proteins. The protein oligomer is modeled as a heterogeneous, freely jointed chain with two possible values of Kuhn length and contour length representing its folded and unfolded configurations. We obtain analytical solutions for the force-extension response of the protein oligomer for different types of loading conditions.