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We study the synchronization of two model neurons coupled through a synapse having an activity-dependent strength. Our synapse follows the rules of Spike-Timing Dependent Plasticity (STDP). We show that this plasticity of the coupling…
Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable…
In this paper, we present a rapidly-prototyped, costefficient, 3D-printed quasioptical sample holder for improving the signal-to-noise ratio (SNR) in modern, resonator-free, highfield electron paramagnetic resonance (EPR) spectrometers.…
We develop a continuum elastic approach to examining the bending mechanics of semiflexible filaments with a local internal degree of freedom that couples to the bending modulus. We apply this model to study the nonlinear mechanics of a…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
Synthetic biology sets out to implement new functions in cells, and to develop a deeper understanding of biological design principles. In 2000, Elowitz and Leibler showed that by rational design of the reaction network, and using existing…
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater…
Spiking Neural Networks (SNNs) have emerged as a promising alternative to traditional Deep Neural Networks for low-power computing. However, the effectiveness of SNNs is not solely determined by their performance but also by their energy…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
For most of the important processes in DNA metabolism, a protein has to reach a specific binding site on the DNA. The specific binding site may consist of just a few base pairs while the DNA is usually several millions of base pairs long.…
Hyperspectral imaging (HI) has emerged as a powerful tool in diverse fields such as medical diagnosis, industrial inspection, and agriculture, owing to its ability to detect subtle differences in physical properties through high spectral…
There exists a significant scale gap between photonic neural network integrated chips and neural networks, which hinders the deployment and application of photonic neural network. Here, we propose hardware-aware lightweight spiking neural…
DNA unzipping by nanopore translocation has implications in diverse contexts, from polymer physics to single-molecule manipulation to DNA-enzyme interactions in biological systems. Here we use molecular dynamics simulations and a…
We show that short-length probabilistic shaping reduces nonlinear interference in optical fiber transmission. SNR improvements of up to 0.8 dB are obtained. The shaping gain vanishes when interleaving is employed and not undone before…
The functioning of double-stranded (ds) nucleic acids (NAs) in cellular processes is strongly mediated by their elastic response. These processes involve proteins that interact with dsDNA or dsRNA and distort their structures. The…
Single-molecule FRET is widely used to study helicases by detecting distance changes between a fluorescent donor and an acceptor anchored to overhangs of a forked DNA duplex. However, it has lacked single-base pair (1-bp) resolution…
Spiking Neural Networks (SNNs) are more biologically plausible and computationally efficient. Therefore, SNNs have the natural advantage of drawing the sparse structural plasticity of brain development to alleviate the energy problems of…
Using Langevin dynamics simulations, we study elastic response of single semiflexible polyelectrolytes to an external force pulling on the chain ends, to mimic the stretching of DNA molecules by optical tweezers. The linear chains are…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…